Since this Wrye Bash Bain thing looks really interesting, I figured I'd re-do my installation and try to use only Wrye Bash and BOSS to order most everything.
Since you guys generally have lots of good suggestions on things to do differently, I figured I'd post my own walkthrough here. Sounds fun to me, anyway. (Also, Delte, you can see how somebody who loves mods but just doesn't know anything about things like TES4edit.)
So, fresh clean Oblivion GOTY install. (Oblivion, GOTY, KotN. I'd have the other addons, but I've never found 'em on hard media.)
Now, I have the UOP and USIP in omod format, so I'll just tell OBMM to convert to archive and stick them safely in Wrye's Oblivion Mods\Bash Installers directory. (The reason why I'm using OBMM to export them is because the way TimeSlip packages the omods is really funky. Yes, technically they're a 7z archive, but the data structure is completely different then "just" a 7z file.)
Now, without even having to do something like open and close Wrye, the 7z file is recognized as a mod. It's got all the esp's I'm interested in, und VOILA! you tell it to install. One of the things I'm liking about this is that I have a list of esp's I can filter BEFORE the first install, instead of extract to a folder, go through by hand, move files, install, find out I missed something, rebuild the omod again, etc.
Wash, rinse, and repeat for USIP.
For the UOMPatches, there's a lot of esp's I can't use. In fact, all I need its the one for knights. Since I can filter what gets installed before installing, this makes it easy!
Now I need to install OOO. And then the OOO patch. So, since I don't need the esp and esm from OOO1.33, I'll just filter them out. (Because it's easy.) OOOhh.. (Sorry, I know, that was bad) I can highlight multiple modules and install them at once! This is something I've always wanted OBMM to have, since frequently there's five mods that don't conflict that I want to install as a batch.
But wait - the icon for OOO is yellow. It has 18 conflicts! What files are conflicted!? This could be really useful.
meshes\armor\cowlofthegrayfox\helmet_gnd.nif
meshes\armor\dwarven\m\greaves_gnd.nif
meshes\harvest\containers\XMSmiddlepaintingforest02b.nif
meshes\Weapons\Meteoric\met2hmace.nif
meshes\Weapons\Meteoric\metbow.nif
meshes\Weapons\Meteoric\metmace.nif
meshes\Weapons\Meteoric\metscimitar.nif
meshes\Weapons\Meteoric\metssword.nif
meshes\Weapons\Meteoric\metstaff.nif
textures\menus\icons\weapons\meteoric\metgreatmaceico.dds
textures\menus\icons\weapons\meteoric\metmaceico.dds
textures\menus\icons\weapons\meteoric\metscimitarico.dds
textures\menus\icons\weapons\meteoric\metsswordico.dds
textures\menus\icons\weapons\meteoric\metstaffico.dds
textures\weapons\hf1\steelclaymore_n.dds
textures\weapons\hf1\steellongsword_n.dds
textures\weapons\hf2\steelclaymore_n.dds
textures\weapons\hf2\steellongsword_n.dds
Hey, wait - aren't most of these fixed by the unofficial oblivion patch? A useful excerpt from the manual:
Install Order
? When you install a package, then the order of higher packages will be respected. I.e. if the package being installed conflicts with a higher order package that's already active, then it won't overwrite the files from the higher package. Rather, only the files that don't conflict with higher packages will be installed. (However, if you want to overwrite later packages, then you can use the "Install Last" command, which will move the selected packages to the end of the list and then install them.)
That's just awesome. Bash 3 (One extra point for an ordered conflict list, instead of listing the conflicting mod per file, which makes it hard to parse quickly) and OBMM 0.
Hmm. Lets test this.
I've just marked MMM 355 as 0, 355b5 as 1, and 3.7b as 2. Install them all at once...
Sure enough, all it installs from 355b5 is one nif file for a shirt.

hahaha, that's awesome.
The annealing process it has is pretty sweet as well. This makes my life much, much easier. (OBMM is supposed to be able to back up and restore files correctly. In my experience, it does not always do so.)
I assume most of you have, at some time or another, had somebody hit you with a great big WTF!?!? I'M A MISSING MESH at some time or another. Tracking down missing meshes is, in my experience, a royal pain - what mod does item X come from? etc.
So lets uninstall MMM 355b1 and have BAIN do a scan. No wait, the file's still there. Um. *rummage* Aha! If I delete it by hand, and then do a partial (not even a full) rescan, which only takes less than a minute, it finds it's missing. Also, there's a command to only install missing files. That's so awesome.
When I uninstalled it, it automatically annealed the shirt.nif in question in from MMM 3.55.
Okay, so lets try doing a batch install of things.
I mean really doing a batch install of things.

First, Francesco's. It comes in these exe installer files, but that's not going to work for BAIN. However, we can specify the directory we want it to install to - and voila! 7z it up, stick it in the BAIN installers directory, and poof. Frans package for BAIN. So easy. (This way, it'd be easy to install Fran's with ALL options, and just disable the ones you don't want on the fly. Hmmm.) So.
Francesco's Leveled Creatures-Items 4.5b
Oblivion Warcry 1.08b
Oblivion Warcry 1.085b patch
Bob's Armory
Loth's Blunt Weapons
Unofficial Fran's armor addons
Unofficial level 30+ fran's goodies
Now, admittedly, I did do some repackaging so the directory structure is what BAIN expects. However, I can do that in my sleep and not break my Oblivion install.

(I also converted the .rar's into .7z's - 7z is a superior compression algo by far. Like, figure an additional 25% compression or so.)
The fact that if I have an esp or esm installed that I don't want, all I have to do is uncheck it and anneal and things are fixed, as opposed to rebuilding an omod or desyncing OBMM.
So far, this plus BOSS is equating to no need at all for OBMM.
I'm quite amazed.
Plus, if I need to install something later that needed to be installed much earlier, it's easy now - Tell it where to go in the list, select the esms/esps you need, anneal any that need it. Seems to do it automatically as part of the install, actually.
Okay. I'm sold on this BAIN thing!
Exnem's runeskulls always seemed like an unbalancing concept, but the pictures look pretty. Since this is so easy, I'll throw it in. It's easy to take out now.

Well
I kinda forgot to keep typing here I got so into it XD
AHHHH!!!!!
If you make a directory and copy other packages into it, you have a COMPLEX PACKAGE WITH SELECTABLE SUBPACKAGES.
>.>
I now have a package, "Sjadows Oblivion Sound Overhaul Selections" which contains MIS, MIS Edited, OSSO, Sounds & Storms, Audia Arcanum 2.0 and 2.1, and footsteps of heroism... BECAUSE I CAN!
Okay, it's obvious I've gotten distracted by the shiny new toy. *cough* So here's the simplified version of what I have installed:
USIP 1.4
USIP MODS FCOM patch (also 1.4 of course)
UOMP 1.5 (for KotN)
UOMP 1.5 MOBS
UOP 3.2.0
OOO 1.33
OOO 1.34 Beta 5
MMM 3.5.5 full
MMM 3.5.5 Beta 5
MMM 3.7 Beta and MMM for SI
Francesco's levelled items creatures 4.5b
OWC 1.08b
OWC 1.085b patch
Bobs Armory Oblivion 1.1
Loth's Blunt Weapons v3
Frans Armor Addon v2 + ordinator armor + bonemold helm resources
Frans level 30+ items
Exnem Runeskulls (If it makes me rich or overly powerful even after being nerfed, I'm dropping this)
FCOM Convergence 0.9.9 beta
FCOM Entropic Order rebalance
Streamline 3.1
More Immersive Sound v1.d
More Immersive Sound Edited by Brumbek v1.0
Oblivion Stereo Sound Overhaul by PsychEroc 0.9
Audia Arcanum Sound Overhaul by IlmrynAkios 2.0, 2.1, and FootSteps of Heroism
Storms and Sounds by Deathless Aphrodite and lilith v3
DarkUId DarN v1.6
DarkUId DarN recolour by Luchaire v1.5.5
Atmospheric DarkUI Loading Screens by Galahaut
COBL
COBL cosmetics res
Eyecandy Variants Expansion for HGEC (Modifies clothing/armor from stock, mmm, ooo, frans, fcom, armamentarium, etc for custom bodies)
NECs high-res textures (Gets rid of blockyness on the textures, I'm just running the 2048x2048's)
Alive Waters by Windsurfer v0.6
Supreme Magicka v0.88d (Because trying to play a mage in FCOM? Freaking impossible, you can't even get from the sewers TO vilverin unless your mage can sneak. Even then, I summoned a skeleton like 40 times just to kill 3 bandits, and almost died killing a bandit WHO HAD NO ARMOR after he was half dead already!)
Unique Landscapes. (Because vanilla was, well, vanilla.)
* NOTE - I built UL as a complex package. Excessively long file names like C:\Users\Your_Name\Desktop\Bethesda Softworks\Oblivion Mods\BASH Installers\Special Unique Landscapes BAIN package\Brena River Ravine by chuck21 Arthmoor IAMTHEEMPEROR v1.0.2\ cause Wrye BAIN to have a problem finding things. Then the file gets stuck in the installertemp folder, and even if you correct the pathing issues, it finds files with the same crc's in the installertemp folder and tries to use them. Which causes it to freak out again.

Just so you know.
OBGE - This, since it's effectively just a .dll file, has to be installed by hand (i.e. I REALLY WANT THIS) because BAIN will skip batch files, dlls, exes, etc. for safety.
Enhanced Water SI 2.0
Enhanced Weather 1.3
Enhanced Weather 1.3.4 patch
Screeneffects by qzilla 1.0
Ambient Dungeons by KalendraStar v1.2.2
Rainbows in Tamriel by Deathless Aphrodite v3.0
Realistic Health by abo v2.2. (HI ABO!)
Realistic Fatigue by abo v1.2 (Still love your mods)
Realistic Levelling by abo v1.12 (Finally replaced my antique AFLevelmod with this.)
TIE-In by Ulrim v1.2 beta 3.
Unfathomed Tower by Trollf. (c'mon, it's by trollf.)
Now, while installing all of these, I've taken great care to try and only select the esms/esps I need. However, lets consult BOSS - and it gives me the following problems:
Cobl Tweaks.esp
!!! FCOM INSTALLATION ERROR: Delete. Already included in 'FCOM_COBL.esp'.
Item interchange - Placement.esp
!!! FCOM INSTALLATION ERROR: Delete. Use II's 'Item Interchange - Placement for FCOM' instead.
Looks like I made two mistakes total. Not bad - And easy to fix with BAIN. (If it were a manual install, I'd just delete. However, what if I deleted the wrong thing? Going back and forth with a file like OOO that takes a long time to decompress is such a pain.

And, should I ever need to rebuild the data directory again, it's insanely simple. Delete Data, copy my backup from the fresh install over.. BATCH INSTALL EVERYTHING because it remembers things like what esps I have unchecked.

Okay. Wrye BAIN got my vote!
Now, I'm using 54 mods (Just getting started lol - You'll notice I don't have any hunger/sleep mods yet, for instance, nor have I installed any texture packs - so far I've kept it down to a fairly small 2.61GB of 7z files.) I've only got 183 files/dirs in my Data dir.

Lots of these mods don't particularly like each other. That's what the Bashed patch is for.
Now, because I'm using Wrye bash, it's trivial to find out I'm missing 'you are here.esm' which ambient dungeons depends on - Guess I didn't read that well enough.

so add that to the list. (Much better then "Hey, I wonder why Oblivion CTD's on start.)
It should be noted that item interaction is an exception. It's one of the few mods you'll ever use with missing masters, because it can *only* be used with bashed patches - it never actually gets to be active, as far as oblivion is concerned. One feature I'm not using right now is the ability of Wrye Bash to import a number of incompatible, say, eye mods. Yes, Wrye Bash can even help fix googly eye problems. (However, using both COBL races and Beautiful People was pushing it when I last tried it a year ago - lol. You could get it to work with some tinkering though.)
I now have a total of 96 things loaded, as far as Oblivion is concerned. Of course, lets go over it once more thoroughly with the tools at hand.
Hmmm. FCOM_TamrielTravellers should be removed, I didn't install that. Pulled. I forgot to pull that extra item interchange. Pulled.
Everything else looks good, for a rabid rush to install some random huge number of mods quickly with a new tool. In fact, it's much, much cleaner than the installs with OBMM, because repacking omods takes a long, long time, and so getting all the extra files out takes 10x as long as using BAIN does. As long as you're happy with defaults, there's not even any file editing. (I'm looking at you, Delte. Sheesh, do it all by hand but get all shivery at the parts that have to be done by hand... hehe

Congratulations! I have created a crash on load / crash on start new game problem! But we can get to the main menu just fine.
Lets uninstall some things. Lots of things.
... What do you mean, permission denied? it's my file. Also, nothing is accessing it. Ah, the joys of running windows 7 RC. Lemme reboot.
Nope, still a permission denied. Hrm. Let me check the security tokens on said file.
How the devil did footsteps of heroism get flagged READ ONLY!? If Oblivion tries to open files RW by default, that would explain a _lot_ about why it corrupts itself sometimes. Let me rebuild that. We also have a ton of missing files. I've been seeing this alot lately. Either I've got a RAM problem, or windows 7 RC VFS is screwy as hell.
*Does a bulk uninstall, then starts smaller batch installs, fixes a low-level issue with his solid state drive*
Oh hay, the DarkUId DarN recolor is breaking it. That's odd. Ah! Despite having no esp's / esm's, the install order needs to be DarkUId DarN, recolor, atmospheric screens.

Easy to adjust on Wrye BAIN, and if I uninstall everything and reinstall it all at once... The install order is honored.
So lets summarize what I just did: I installed 54 mods, crashed oblivion 3 or 4 times getting the issue with the menus modifiers sorted out, und voila. I have a fast-loading, fast-exiting oblivion that doesn't crash.
I repeat.
It does not crash on exit.
It exits quickly.
I'm running obse, obge, etc.
I think that right there says why wrye bashed patches and BOSS are considered so very, well, required, by so many players.
Delte - ordering modules for use with Wrye bashed patches can be different from how you'd order them if conflicts still caused one to win and one to lose all the time. For your consumption:
Active Mod Files:00 Oblivion.esm01 ScreenEffects.esm02 Francesco's Leveled Creatures-Items Mod.esm03 Francesco's Optional New Items Add-On.esm04 EnhancedWeather.esm [Version 1.3.4]05 Cobl Main.esm [Version 1.70]06 Oscuro's_Oblivion_Overhaul.esm [Version 1.34]07 Mart's Monster Mod.esm [Version 3.7b1]08 FCOM_Convergence.esm [Version 0.9.9a7]09 You Are Here.esm0A Cobl Races.esp [Version 1.52]0B Cobl Races TNR.esp [Version 1.53]0C Cobl Races TNR SI.esp [Version 1.53]0D Unofficial Oblivion Patch.esp [Version 3.2.0]0E UOP Vampire Aging & Face Fix.esp [Version 1.0.0]0F Oblivion Citadel Door Fix.esp10 DLCShiveringIsles.esp11 Unofficial Shivering Isles Patch.esp [Version 1.4.0]12 Francesco's Optional Chance of Stronger Bosses.esp13 Francesco's Optional Chance of Stronger Enemies.esp14 Francesco's Optional Chance of More Enemies.esp15 Francesco's Optional Leveled Guards.esp++ FCOM_Francescos.esp [Version 0.9.9]++ FCOM_FrancescosItemsAddOn.esp [Version 0.9.9]16 FCOM_FrancescosNamedBosses.esp [Version 0.9.9]17 Fran Armor Add-on.esp18 Fran_Lv30Item_Maltz.esp19 Atmospheric Loading Screens - Random Quotes.esp1A EnhancedWeather.esp [Version 1.3.4]1B EnhancedWeather - SI.esp [Version 1.3]1C EnhancedWeather - Enhanced Seasons.esp [Version 1.3.1]++ EnhancedWeather - Darker Nights, 80.esp [Version Final]1D Enhanced Water v2.0 HD - SI Addon.esp [Version 0.1]1E Symphony of Violence.esp1F MIS.esp20 MIS Low Wind.esp21 MIS New Sounds Optional Part.esp22 Atmospheric Oblivion.esp23 Rainbows.esp24 AmbientDungeons.esp [Version 1.2]25 AliveWaters.esp26 AliveWaters - Koi Addon.esp27 AliveWaters - Slaughterfish Addon.esp++ Item interchange - Extraction.esp [Version 0.71]28 P1DmenuEscape.esp29 ExnemRuneskulls.esp++ FCOM_ExnemRuneskulls.esp [Version 0.9.9]2A Cobl Glue.esp [Version 1.69]2B Cobl Si.esp [Version 1.63]2C OOO 1.32-Cobl.esp [Version 1.69]++ FCOM_Cobl.esp [Version 0.9.9]++ Cobl Tweaks.esp [Version 1.44]2D Bob's Armory Oblivion.esp2E FCOM_BobsArmory.esp [Version 0.9.9]2F Loth's Blunt Weapons for Npcs.esp++ FCOM_LothsBluntWeapons.esp [Version 0.9.9]30 Oblivion WarCry EV.esp31 FCOM_WarCry.esp [Version 0.9.9]32 Oscuro's_Oblivion_Overhaul.esp [Version 1.34]33 OBSE-Storms & Sound SI.esp34 FCOM_Convergence.esp [Version 0.9.9]35 FCOM_OscurosOverhaul.esp [Version 0.9.8]++ FCOM_EntropicOrderRebalance.esp [Version 0.9.9beta2]36 FCOM_RealSwords.esp [Version 0.9.9]++ FCOM_SaferRoads.esp [Version 0.9.9]37 Mart's Monster Mod - Extra Wounding.esp [Version 3.7b1]++ Mart's Monster Mod - Looting NPCs & Creatures.esp [Version 3.7b1]38 Mart's Monster Mod - Zombies for Body Meshes.esp [Version 3.7b1]39 Mart's Monster Mod - Vindasel.esp [Version 3.7b1]3A Mart's Monster Mod - Foxes.esp [Version 3.7b1]3B Mart's Monster Mod - Dungeons of MMM.esp [Version 3.7b1]3C Mart's Monster Mod - Hunting & Crafting.esp [Version 3.7b1]3D Mart's Monster Mod - Farm Animals.esp [Version 3.7b1]3E Mart's Monster Mod - Durzog Addon.esp [Version 0.10]++ FCOM_DiverseGuardUnity.esp [Version 0.9.9]++ FCOM_BobsGuardUnity.esp [Version 0.9.9]++ FCOM_Archery.esp [Version 0.9.9]++ FCOM_FriendlierFactions.esp [Version 0.9.9]3F FCOM_MoreRandomSpawns.esp [Version 0.9.9]40 FCOM_MoreRandomItems.esp [Version 0.9.9]41 TIE In.esp [Version 1.2b]++ TIE In - ExnemRuneskulls.esp [Version 1.2b]++ TIE In - Cobl.esp [Version 1.2b]42 TIE In - FCOM Convergence.esp [Version 1.2b]++ TIE In - RealSwords.esp [Version 1.2b]++ TIE In - MMM Craft.esp [Version 1.2b]++ TIE In - DiverseGuardUnity.esp [Version 1.2b]++ TIE In - BobsGuardUnity.esp [Version 1.2b]43 Mart's Monster Mod - Shivering Isles.esp [Version 0.18]++ Fransfemale.esp44 OOO-WaterFish.esp [Version 1.34]++ MMM-Cobl.esp [Version 1.69]45 UnfathomedTower.esp46 Knights.esp47 Knights - Unofficial Patch.esp [Version 1.0.9]++ Mart's Monster Mod - Knights.esp [Version 3.7b1]++ TIE In - Knights.esp [Version 1.2b]48 Mart's Monster Mod - City Defences.esp [Version 3.7b1]++ FCOM_Knights.esp [Version 0.9.9]49 xuldarkforest.esp [Version 1.0.2]4A xulStendarrValley.esp4B xulTheHeath.esp4C XulEntiusGorge.esp4D ULFallenLeafEverglade.esp4E xulColovianHighlands_EV.esp4F xulChorrolHinterland.esp [Version 1.2.1]50 xulBeachesOfCyrodiilLostCoast.esp51 xulBravilBarrowfields.esp [Version 1.3]52 xulLushWoodlands.esp [Version 1.3]53 xulAncientYews.esp54 xulAncientRedwoods.esp [Version 1.6]55 xulCloudtopMountains.esp56 xulArriusCreek.esp57 xulPatch_AY_AC.esp [Version 1.1]58 xulRollingHills_EV_withoutWheat.esp [Version 1.3.2]59 xulRollingHills_EV.esp [Version 1.3.2]5A xulPantherRiver.esp5B xulRiverEthe.esp5C xulBrenaRiverRavine.esp [Version 1.0.2]5D xulImperialIsle.esp [Version 1.6.1]++ FCOM_UnofficialFranArmorAddon.esp [Version 0.9.9]5E Salmo the Baker, Cobl.esp [Version 3.08]++ TIE In - Salmo, Cobl.esp [Version 1.2b]5F RealisticFatigue.esp60 RealisticHealth.esp61 SupremeMagicka.esp [Version 0.88]62 SM_ShiveringIsles.esp [Version 0.86]++ SM_OOO.esp [Version 0.87]++ SM_MMM.esp [Version 0.82]++ SM_COBL.esp [Version 0.86]++ SM_AbsorbRestoration.esp [Version 0.80]63 SM_EnchantStaff.esp [Version 0.80]++ SM_UnlockSpells.esp [Version 0.70]++ SM_Scrolls.esp [Version 0.84]++ SM_SigilStone.esp [Version 0.83]64 RealisticLeveling.esp++ Item interchange - Placement for FCOM.esp [Version 0.71]++ Mart's Monster Mod - Resized Races.esp [Version 3.7b1]65 Cobl Silent Equip Misc.esp [Version 01]66 Streamline 3.1.esp++ EVE_StockEquipmentReplacer4FCOM.esp++ EVE_KnightsoftheNine.esp++ EVE_KhajiitFix.esp67 EVE_ShiveringIslesEasterEggs.esp68 Bashed Patch, 0.esp
P.S. ++ means the mod isn't actually loaded as a mod by oblivion. All of its content has been merged into the bashed patch. For lots of other things, especially levelled lists, are imported into the bashed patch.

So, in summary, I've decided I very enthusiastically like Wrye BAIN. In fact, I'm now using it instead of OBMM, which I expect I'll eventually remove from the system completely.
Anybody have any questions?