Okay, I think that, instead of putting everything together and try to fix all of the inevitable errors, I think it would be better to discuss the mod set-up I'm wanting to use first.

Here's the list of mods I'm hoping to use.

Fallout 3 Re-Animated

Fallout Street Lights

RH_IronSights

Scavanger Armors

DCInteriors Project

Firefly Ranch - Scary Quest Edition

Franklin Mall

RR Companions Vault

Shadows and Dust 1 & 2

Cybernetics Perk Tree

Perk Steroids

T-2000 Perk

Sydney Follower

TERMINATOR Cybernetic Dawn

Ties that Bind

Abbreviated Effects

Ambient Temperature

Ammo Press at Megaton House

CRAFT

EMP Damage for Power Armour

Enhanced Weather

EVE

Fallout Interoperability Program

Fallout Legacy Perks

Fellout

FNNCQ a fallout 3 slavery overhaul

FO3 Wanderers Edition

Genetic Freak Perk

Imps More Complex Needs

Impervious Power Armour

Marts Mutant Mod

MMM- Monsters perks addon

MTC Wasteland Travellers

Nanotech Perk Pack

New Vegas Perks

No Repair With Uniques

Prebuilt MyImperviousArmors list

Scope Master Perk

See you - Time for Bed

Silver Slugger Melee Perk

Ultimate Perk Pack

Weapon Mod Kits

Weight Lifter Perk

Youre SPECIAL

Enclave Improvement Project

MERC 2

Basic Cooking Perk

Fallout Stutter Remover

Unofficial Fallout 3 Patch

Enhanced Blood Textures

Enhanced Night Sky

eXcalibr

Flora Overhaul Total Devastation Edition

Hi-Res Weapons

NMCs_Texture_Pack

A World Of Pain

Alton IL

Arefu Expanded

My Utility World

Raiders Redone

Wasteland Guards aka DC Defence

Official Fallout 3 Patch

A Note Easily Missed

A Quest for Heaven 1 & 2

An Evening With Mister Manchester

Cube

In the Shadow of the Swamp

The Crimson Caravan

The Institute

The Mantis Imperative

Vault 101 Revisted

CONELRAD 640-1240 - Civil Defense Radio

Existence 2_0

GNR Enhanced

MTUI

ArchiveInvalidation Invalidated

12 new uniques for Point Lookout

20th Century Weapons (possibly 19th and 20th century)

Ammunition Schematics for FWE-WMK-CRAFT-Full CalibrV1_4

Box Magazine XM1014 Shotgun

CALIBR1.4

Classic Fallout Weapons

EMP Weapons

EMPulse Weapons for FWE 603 and WMK for FWE

Godfathers Kewl Unique Weapons

Mose Unique

Unique Guns Arsenal Mod

Unique Junk

Weapon Mod Kits - Unique

Do any of these mods clash with other? Do some of these mods need mods I don't have? Will those additional mods clash with the mods on the list?

I know this is a lot, but it's still under the hard plugin limit, and I managed to get Skyrim working with about this many mods, if not more (albiet with duplicate item crafting recipes), so I'm not too concerned about this many mods not working.

Okay, let's hammer out the details and then the mod-order should be easy as cake (knock on wood)

Add the mods one at a time and test the game with each addition.

And, yes, some of these mods will conflict with the other ones. Especially since they are changing the same things. I am not going to give you specific advice on which ones as it looks like you just picked a bunch of them without much thought to how they are going to work together. For example, do you really need 6 or 7 Perk Mods? Some of those quest mods affect the same locations too.

Good luck, and please don't throw all of these at the game at once. Some of them will break the game in combo with others.

Which quest mods effect the same location?

I believe DC interiors and A world of pain might need a patch to work well together. Also it is likely those two mods might have an effect to new quest mods since they might use one of the buildings or areas that one of those two mods have made so you might see a glitch where a door has two names on it. You would have to move the cursor to a specific spot on the door to get the correct location but chances are you might encounter that the game will just crash when getting close to that location.

I have not played FO3 for a few weeks and do not remember which mods I was using at the time. I do remember having both DC Interiors and A world of Pain working at the same time I just do not remember if I needed a compatibility patch or if it was an option to get it at one of those two mod pages.