Over the course of the few years that I have been actively modding (for myself) Fallout 3 I have come across the most stable load order that you will ever use because I have hand-tested for hours on end with several playthroughs and no major issues.

Furthermore, all my TWPC patches are based on my own load order and it is essential that you follow it should you wish to get the same results that I do.

In short, you can have any of your mod .ESM and .ESP files in a specific order you deem fit from another source other than my own BUT my TWPC .ESP files need to be loaded AT THE END of ALL your other mods to ensure maximum compatibility and the patches to do as they were meant to. Failure to do so, and also not following the below load order, may result in undesirable results.

So PLEASE, trust me on this one, sort your load order to the T as I have below and your issues should lessen already, and have far less incompatibilities. Of course I cannot have every single mod listed and these are of my own personal collection of several years which give Fallout a HUGE overhaul, staying mostly lore-friendly and best of all; working together.

This list may change over time and become updated or new mods added, conflict/error ones removed etc. So feel free to ask any and all questions. Just please note that I am not your load order sorter, BOSS/LOOT do exist for this and while they are nowhere as accurate as I would be due to human conflict resolution, I will try to help as best I can if I am not swamped with IRL/patch stuff.

A note on Bashed/Merged patches: When you create them DO NOT include ANY of my TWPC patches!! They are never to be overridden or added to, just batch/merge without them, then ensure said files are loaded BEFORE the TWPC patch files and then activate all my TWPC files.

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Fallout3.esm
Anchorage.esm
ThePitt.esm
StreetLights.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm
Unofficial Fallout 3 Patch.esm
CALIBR.esm
Advanced Recon Tech.esm
aHUD.esm
iHUD.esm
Point Lookout Reborn.esm
Crowded Cities Redux.esm
WastelandGuards01.esm
Vault 101 Revisited.esm
Mothership Crew.esm
TheInstitute.esm
ArefuExpandedByAzar.esm
tubrrCompound.esm
GeorgetownExpansion.esm
DCInteriors_ComboEdition.esm
RiversideCafe.esm
Mart's Mutant Mod.esm
Project Beauty.esm
EVE.esm
AWorldOfPainFO3.esm
CRAFT.esm
FO3 Wanderers Edition - Main File.esm
Detect Traps.esm
Enhanced Weather - Rain and Snow.esm
Xepha's Dynamic Weather.esm
RH_IRONSIGHTS.esm
xCALIBR.esm
20th Century Weapons.esm
MTCBigTownRobotFix.esp
YearlingBooks.esp
UF3P - Exotic Caravans.esp
Zeta Turret Drone Karma Fix - MMM Merged.esp
krzymar-MoonSize_120%.esp
DarNifiedUIF3.esp
FO3 Wanderers Edition - Main File.esp
FO3 Wanderers Edition - DLC Anchorage.esp
FO3 Wanderers Edition - DLC The Pitt.esp
FO3 Wanderers Edition - DLC Broken Steel.esp
FO3 Wanderers Edition - DLC Point Lookout.esp
FO3 Wanderers Edition - DLC Mothership Zeta.esp
FO3 Wanderers Edition - Optional Restore Tracers.esp
UUF3P - FWE Patch.esp
DLM_AgathasSongAutocompleteQuestsFix.esp
FWEAlienWorkBenchFix.esp
Chems and Meds Re-Textures Pack.esp
RubblePilesFix.esp
majormodder's Junk Food to Barbeque Crisps.esp
HDRealWorldWater.esp
schematics2.esp
Laurens_Bathroom_poetry_V1.esp
Fo3HirezdFlamer.esp
Fo3HirezdMinigun.esp
bzArmour.esp
FO3 Wanderers Edition - More Gore.esp
BBBackpacks-v1-1.esp
Advanced Recon Tech - Detect Traps.esp
Detect Traps - DLC.esp
Detect Traps - Perk.esp
Detect Traps - The Traponator 4000.esp
Advanced Recon Gear.esp
Advanced Recon Tech.esp
Advanced Recon Tech FWE.esp
Advanced Recon Range Finder.esp
NightvisionGoggles(Powered).esp
BM19DisablePipBoyGlove.esp
DynamicCrosshair.esp
Stimpak Counter.esp
JIP Realistic Weapon Overheating.esp
JIP Selective-Fire.esp
JIP Companions Command & Control.esp
AutoGates.esp
CASM.esp
Sealurk Radioactive Bites & Stings v2.esp
HumanFleshAddiction.esp
Revamped Leveling - FWE.esp
UPP - Pack 1.esp
UPP - Pack 2.esp
UPP - Experience Perks.esp
UPP  - Quest Perks.esp
Dree Perks.esp
WeaponModKits.esp
WeaponModKits - OperationAnchorage.esp
WeaponModKits - ThePitt.esp
WeaponModKits - BrokenSteel.esp
WeaponModKits - PointLookout.esp
WeaponModKits - Zeta.esp
WeaponModKits - FWE Master Release.esp
WeaponModKits - FWE Talon Loot Crash Fix.esp
RH_FWE_Bridge.esp
RH_WMK_Bridge.esp
PlasmaRifleAwesomefiedWMK.esp
xCALIBR_20CW_v5.12.esp
CALIBRv14 Ammunition Schematics for FWE-WMK-CRAFT-V1_3-18639.esp
20th Century Weapons -Plus- Reborn FWE-WMK-Calibr14_V1_70RC_18668.esp
20th Century Weapons -Plus- Reborn Cut Weapons.esp
20th Century Weapons -Plus- Reborn xCALIBRized + RHIron.esp
ZL-SVD-CALIBR.esp
SVDForFWE.esp
IMPACT.esp
K9Breeds.esp
K9BreedsMoreDogs.esp
K9BreedsPatchDLCPitt.esp
lexx_brahmin-variant-Fo3.esp
FeralGhoulTest.esp
GlowingGhouls-MMM.esp
Distributed Necklaces and Chains - Males and Females.esp
Project Beauty- Broken Steel.esp
Project Beauty- Point Lookout.esp
PAL - MERGED.esp
MoreMapMarkers.esp
DIFF.esp
Lookout Outfits.esp
T3_leather armors.esp
Tattered_suits.esp
Freebooter_Armor.esp
Trooper_outfits.esp
Scout Outfits.esp
Tribal_DX.esp
WinterizedT51bDX.esp
Bornagain Reillys Rangers Helmet Texture Patch.esp
Bornagain Zeta Combat Armor Texture Patch.esp
BornAgain Outcast v3.esp
Dragonskin Tactical Outfit.esp
DragonskinBonusPack.esp
Dragonskin_for_FWE_2014.esp
ArefuExpandedByAzar-Radio.esp
tubRRCompound.esp
NotSoFast.esp
HeirApparent.esp
IntoTheDeepWoods.esp
PLFewerItems.esp
PLweightadjust.esp
The Mantis Imperative - Mantis.esp
The Mantis Imperative - Jello.esp
The Mantis Imperative - Nasty Zeta No Scaling.esp
Existence 2.0.esp
NewMall.esp
Arbor.esp
TrentonTowers.esp
Mart's Mutant Mod - DC Interiors.esp
BaileysCrossingMetro.esp
Big Town Overhaul [GangStore].esp
Big Town Overhaul - Fallout Street Lights - Compatibility Patch.esp
Better RC Church.esp
CanterburyCommonsInteriors.esp
Kentbury Way.esp
MetroCars.esp
Museum.esp
FortIndependenceRedesigned.esp
PotomacSteamworks.esp
Temple of the Union Overhaul.esp
UrgeWashingtonBoS.esp
UndergroundHideout.esp
7_HolsterForHandGunsV1_1.esp
PointRadio.esp
Gunfire Sound Range Increased - Core + DLC + EVE + FWE.esp
GNR Enhanced.esp
Flora Overhaul.esp
PureWater-VeryCleanLittleRad-.esp
Fellout-Anchorage.esp
Fellout-BrokenSteel.esp
Fellout-Zeta.esp
Fellout-pipboylight.esp
megalight.esp
Realistic Interior Lighting.esp
Enhanced Weather - Weather Sounds in Interiors.esp
DC Moods.esp
The  Pitt Moods.esp
PointLookout Moods.esp
Xepha's Dynamic Weather - Main + DLC Merged.esp
Xepha's Dynamic Weather - Dynamic Sneak Bonus.esp
Xepha's Dynamic Weather - Green Tint Remover.esp
Xepha's Dynamic Weather - Rain.esp
Xepha's Dynamic Weather - Sandstorms + Armor Damage (FOSE).esp
Xepha's Dynamic Weather - Weather Machine (Start Game Added).esp
IMPACT RH_IS+FWE+WMK+All DLCs.esp
Blackened FWE + MMM + EVE + Project Beauty.esp
Blackened RH + FWE + EVE.esp
Immersive First-Person Messages - Vanilla.esp
Merged Patch.esp
Bashed Patch, 0.esp
(TWPC) DIFF-UUF3P-FWE Patch.esp
(TWPC) HFA-UUF3P-FWE Patch.esp
(TWPC) RBS-MMM Patch.esp
(TWPC) RBS-MMM-FWE Patch.esp
(TWPC) MMM-UUF3P-FWE Patch.esp
(TWPC) MMM-EBTMG-FWE Patch.esp
(TWPC) HRWW-DIFF-UUF3P-FWE Patch.esp
(TWPC) BFM-UUF3P-FWE Patch.esp
(TWPC) BFO-FWE Patch.esp
(TWPC) BFO-MMM-UUF3P-FWE Patch.esp
(TWPC) BFO-MMM-EVE-UUF3P-FWE Patch.esp
(TWPC) BVR-FWE Patch.esp
(TWPC) K9B-UUF3P-FWE Patch.esp
(TWPC) TMI-FWE Patch.esp
(TWPC) BBB-UUF3P-FWE Patch.esp
(TWPC) PLR-ISS Patch.esp
(TWPC) BRC-PB Patch.esp
(TWPC) CMRP-FWE Patch.esp
(TWPC) CPW-UUF3P-FWE Patch.esp
(TWPC) GE-UUF3P Patch.esp
(TWPC) PLR-MMM Patch.esp
(TWPC) RRE-FWE.esp
(TWPC) RRE-PB-BLACKENED-FWE Patch.esp
(TWPC) TCC-UUF3P-FWE.esp
(TWPC) TCC-MMM-UUF3P-FWE.esp
(TWPC) TD-FWE Patch.esp
(TWPC) UEC-MMM-UUF3P-FWE.esp
(TWPC) UEC-MMM-PB-UUF3P-FWE Patch.esp
(TWPC) UEC-MMM-PB-EVE-UUF3P-FWE Patch.esp
(TWPC) WD-UUF3P-FWE Patch.esp
(TWPC) WD-DIFF-UUF3P-FWE Patch.esp
(TWPC) WST3BFM-PB Patch.esp
(TWPC) Arbor-UUF3P-FWE Patch.esp
(TWPC) RIL-UUF3P-DM Patch.esp
(TWPC) DM-UUF3P-DW Patch.esp
(TWPC) DIFF-RI-EVE-MMM-WMK-PRA-F3HMG-F3HF-20CWRE-IMPACT-UUF3P-FWE Patch.esp
(TWPC) WMK-UUF3P-FWE Patch.esp
(TWPC) 20CWRE-WMK-UUF3P-FWE Patch.esp
(TWPC) 20CWRECW-UUF3P-FWE Patch.esp
(TWPC) 20CWRE-UUF3P-FWE Patch.esp
(TWPC) 20CWRE-WMK-RIFWC-UUF3P-FWE Patch.esp
(TWPC) 20CWRECW-WMK-RIFWC-UUF3P-FWE Patch.esp
(TWPC) PRA-FWE Patch.esp
Deadmano's Custom Patch.esp