Redeye and Pysmon - I use the wrye flash now and its funny, I have removed most conflicts by tagging certain mods (trial and error) and can play without masterupdate without crashing ingame or exit...when I get my final mod list together, I probably will masterupdate it all. So my point may be that wrye flash might be the only way to go with 100 or more mods loaded....
However, I see you both use a couple of mods I know nothing about and are these stable mods to add (dont want to highjack thread but we are talking about stability):
Well, I suppose I will grab this first chunk since it looks like most of those come from my listing
Princess Better Prompts v1pt1.esp
Personally, I love this mod, and I have had no issues with it in my game whatsoever as of yet (though I will be fair, I have not gotten to the point of fully completing the game with it in, so there COULD be problems later on, but nothing I can see in there makes me suspect I will have issue). It will obviously have potential conflicts with other mods that would adjust player dialogue options, but if you just load it early then there should be no real problems. Also, the changes in this are very minor, but they are very welcomed, IMO.
Treasure Maps_Underground.esp
Treasure Maps_Secrets of the Wasteland.esp
Treasure Maps_Bobblehead Edition.esp
Treasure Maps_A Fist Full of Caps.esp
These have been as stable as can be for me, and a certainly an interesting addition to the gameworld. If you do ever get conflicts with these, at worst it would be not having access to one of the maps or one of the treasure spots due to something being placed over them or whatnot. You won't be getting stability issues with them though, that is for sure.
Destruction - Main.esp
Destruction - Main - Statics.esp
Destruction - DLC.esp
Destruction - DLC - Statics.esp
I just recently added the Destruction mod into my load list, and I expect it conflicts with tons of stuff I am using, but I just load it extremely early so that everything else can just override the changes it makes in cases it is needed as this is really just an aesthetic mod to add a little more immersion. I also haven't seen any real noticeable stability or performance issues since I have been using it.
FalloutFood.esp
FalloutFoods - FWE Master Release.esp
This combo has worked flawlessly for me so far, the only thing is that if you use MMM, there is no patch for it to go with this, so you will get some minor inconsistencies (but these could be quickly fixed by making a little patch with FO3Edit).
And a few others I cant find by searching:
URWL.esp
WRWC - Classic Fallout.esp
These are Ultra Realistic Wasteland Lighting (which appears to be removed from download on the Nexus) and http://fallout3nexus.com/downloads/file.php?id=2121, respectively, and both of them have again worked without issue for me what-so-ever. I recently dropped URWL myself (which I may be regretting as I don't think I have a backup) to take a try at Realistic Interior Lighting since I run Dynamic Weather which renders a lot of what URWL is designed for moot.
Not sure about the other ones you mentioned though.