Install the game clean on your ssd, and what I mean by clean is go to Users/?Your User Name?/Documents/My Games and delete the Fallout3 folder, then go to Users/?Your User Name?/AppData/Local and delete the Fallout3 folder, then uninstall the Fallout 3 game and delete the Fallout 3 game folder, then reinstall the game outside of the programs files directory

FO3 BSA Decompressor

FO3 WAV Converter

Fallout Anniversary Patcher

Fallout Script Extender (FOSE)
Current beta version: v1.3 b2

Unofficial Fallout 3 ESM Patcher

Command Extender

lStewieAl's Tweaks
Note - This includes many of his mods, some I will mention is Out Of Memory Fix, Increased Heap Allocation, it all so included F3TF - Fallout 3 Tick Fix, so you will not need to install those mods as long as you are using this one

NVAC - New Vegas Anti Crash
Put the nvac.dll inside your Fallout 3/Data/FOSE/Plugins folder

Updated Unofficial Fallout 3 Patch

Combat Lag Fix (FOSE) 

ActorCause Save Bloat Fix (FOSE)

Use some sort of Archive Invalidation, I use Vortex and it comes with Archive Invalidation built in.

In the stewie_tweaks.ini, they are many settings to look at, I use several, but for stability and performance make sure and enable all of these.

bDontMirrorTexturesInRAM
bNoXPBarInCombat 
bPatchHeapSize 
bQueueSemiAutoShots
bTickFix 

[Heap]
iHeapSizeInMB = 512

[Tick Fix]
bFastExit = 1
bFastResolution = 0
bGetTickCountFix = 1
bRemoveRCSafeGuard = 1

Because of the mod Command Extender we can use a FalloutCustom.ini that will override most settings from the Fallout.ini and FalloutPrefs.ini, so you can just make ini changes directly to the FalloutCustom.ini and not worry about changing settings in the vanilla ones, open up a blank notepad sheet, save it and name it FalloutCustom.ini and place it inside this file directory with the rest of your Fallout ini's, Users/?Your User Name?/Documents/My Games/Fallout3

In your FalloutCustom.ini add these

[General]
bPreemptivelyUnloadCells=1
bUseThreadedAI=1
iNumHWThreads=4
[Display]
bFull Screen=1
[BackgroundLoad]
bSelectivePurgeunusedOnFastTravel then equals 1 like any other setting, Nexus keeps adding a javascript event when I type it right.
[Audio]
iAudioCacheSize=8192
iMaxSizeForCachedSound=1024

And for Enb add these
[Display]
iMultiSample=0
iMaxAnisotropy=0
[BlurShaderHDR]
bDoHighDynamicRange=1
[Water]
bUseWaterDisplacements=0

If you use Vortex mod manager, then add this too and all so make sure and activate Archive Invalidation from the Vortex Dashboard
[Archive]
SArchiveList=Vortex - BSA Redirection.bsa, Fallout - Textures.bsa, Fallout - Meshes.bsa, Fallout - Voices.bsa, Fallout - Voices2.bsa, Fallout - Voices3.bsa, Fallout - Voices4.bsa, Fallout - Sound.bsa, Fallout - MenuVoices.bsa, Fallout - MenuVoices2.bsa, Fallout - MenuVoices3.bsa, Fallout - MenuVoices4.bsa, Fallout - MenuVoices5.bsa, Fallout - Misc.bsa
bInvalidateOlderFiles=1
bUseArchives=1

Fallout 3 Realistic Wasteland Lighting
Main File- Fallout 3 Realistic Wasteland Lighting plus GOTY v1.2
Use only one esp from this mod, one is for the base game, and one is for the base game and all the dlc, assuming you have all the dlc, you use only the  
FO3 RWL GOTY.esp and delete or deactivate the other one.

RADiant Light Overhaul
Main File - RADiant Light Overhaul v1.2

Remove Interior Floating Dust
Main File - Remove Interior Floating Dust v1.0

Accurate NASA Stars
Main File - Accurate Stars 4k v1.0

HD Moon 2K - NASA Satellite Images
Main File - HD NASA Moon 2k v3.0

No Glowing Vultures for ENB's
Main File - No Glowing Vultures

Mr Handy ENB Jet Fumes Fix
Main File - Mr Handy ENB Fix

ENB Hair Fixes (Minimal)
Main File - Minimal ENB Hair Fixes v1.0

Water for Enb
Main File- Water for Enb

Fallout 3 HD Overhaul
Optional File - Fallout 3 HD Overhaul Water v1.0

Make sure you add these to your FalloutCustom.ini for Enb to work
[Display]
iMultiSample=0
iMaxAnisotropy=0
[BlurShaderHDR]
bDoHighDynamicRange=1
[Water]
bUseWaterDisplacements=0

Dynamic Weather
Main File - Dynamic Weather v3.0

Open 2 windows in File Explorer, in the first window make a new folder and name it Data, in the second window extract the Dynamic Weather file, inside the the Dynamic Weather file take the textures folder and the Xepha's Dynamic Weather.esm and place it in your new Data folder, then go inside the Dynamic Weather - DLC folder and place the Xepha's Dynamic Weather - Main + DLC Merged.esp inside of your Data folder, then go inside the Dynamic Weather - Sandstorms folder and place the Xepha's Dynamic Weather - Sandstorms.esp inside of your Data folder, then go inside of the Dynamic Weather - Weather Machine folder and place the Xepha's Dynamic Weather - Weather Machine (Start Game Added).esp inside of your Data folder. Right click on your Data folder and select 7zip, then add to archive, name it Dynamic Weathers.7z and select Ok at the bottom to pack it, when it's done take the archive and drop it into your mod manager and install.

I do not use the rain from Dynamic Weathers, I love the idea, but I do not like the execution, but if you wanted to use it, then all your would need is download the 3rd Main file uploaded on Aug 10 from the Enhanced Weather mod page, extract it and rename the Enhanced Weather - Rain and Snow v2 hotfix b.fomod to Enhanced Weather - Rain and Snow v2 hotfix b.7z and then you can extract that with 7zip as an archive. Once inside add the meshes, textures, and sound folder with the Enhanced Weather - Rain and Snow.esm and the Enhanced Weather - Weather Sounds in Interiors.esp to your new Data folder we created above, then put the Xepha's Dynamic Weather - Rain.esp from Dynamic Weathers in there and pack it.

RADiant Light Overhaul
Main File - RADiant Light Overhaul v1.2

Remove Interior Floating Dust
Main File - Remove Interior Floating Dust v1.0

Accurate NASA Stars
Main File - Accurate Stars 4k v1.0

HD Moon 2K - NASA Satellite Images
Main File - HD NASA Moon 2k v3.0

Subtle Sunglare FX
Main File - Subtle Sunglare FX

No Glowing Vultures for ENB's
Main File - No Glowing Vultures

Mr Handy ENB Jet Fumes Fix
Main File - Mr Handy ENB Fix

ENB Hair Fixes (Minimal)
Main File - Minimal ENB Hair Fixes v1.0

Fallout 3 HD Overhaul
Optional File - Fallout 3 HD Overhaul Water v1.0

Make sure you add these to your FalloutCustom.ini for Enb to work
[Display]
iMultiSample=0
iMaxAnisotropy=0
[BlurShaderHDR]
bDoHighDynamicRange=1
[Water]
bUseWaterDisplacements=0

Weather for ENB - URWLENB FO3
Download this and extract it and delete everything except the Data folder, repack the Data folder with 7zip and drop it into your mod manager and install, disable the URWLENB-002-Interiors.esp

Optional, but how I run this mod is I take the URWLENB-001-Weather.bsa and I use Bethesda Archive Extractor (BSA and BA2) and extract it into loose files and take the new textures, meshes, and sound folder and place it into the Data folder with all the plugins, then I delete the URWLENB-002-Interiors.esp, URWLENB-008-Radioactive Rain and Snow.esp, URWLENB-010-Interior Storm Sounds.esp, and URWLENB-011-Sandstorm Armor Damage (FOSE).esp, then repack that Data folder with 7zip and install

RADiant Light Overhaul
Main File - RADiant Light Overhaul v1.2

Accurate NASA Stars
Main File - Accurate Stars 4k v1.0

HD Moon 2K - NASA Satellite Images
Main File - HD NASA Moon 2k v3.0

Remove Interior Floating Dust
Main File - Remove Interior Floating Dust v1.0

No Glowing Vultures for ENB's
Main File - No Glowing Vultures

Mr Handy ENB Jet Fumes Fix
Main File - Mr Handy ENB Fix

ENB Hair Fixes (Minimal)
Main File - Minimal ENB Hair Fixes v1.0

Water for Enb
Main File- Water for Enb

Fallout 3 HD Overhaul
Optional File - Fallout 3 HD Overhaul Water v1.0

Make sure you add these to your FalloutCustom.ini for Enb to work
[Display]
iMultiSample=0
iMaxAnisotropy=0
[BlurShaderHDR]
bDoHighDynamicRange=1
[Water]
bUseWaterDisplacements=0

Home (reshade.me)
Download the latest version of Reshade, run the ReShade_Setup_5.9.2.exe or whatever the latest version exe is and click Browse and a new file explorer window will pop up then direct it to the Fallout3.exe, whatever drive you have it installed on, mine looks like thisC:\Steam\steamapps\common\Fallout 3 goty once here click the Fallout3.exe one time to highlight it, then select open at the bottom, Select Direct X 9 and Next, Next, On the Effects page, it doesn't matter just tick standard effects to get it installed, you will be deleting those and replacing them with the shaders provided from this mod page.Now go into you game folder and rename the d3d9.dll that Reshade put there to this and delete the reshade-shaders folder and the ReShade.ini
d3d9_reshade.dll

ENBSeries v0.451for Fallout New Vegas and Fallout 3
At the bottom of the screen, click the arrow pointing down, to download, after extract the download, and go into the the folder titled WrapperVersion, and copy/paste only these 2 files into your main game folder steamapps/common/Fallout 3 goty
d3d9.dll
enbhost.exe

Now download my File, from this mod pages files tab, extract it, if using the URWL preset then drop the Marcurios's URWLNV Sun archive into your mod manager and install, then inside of the Fallout 3 goty folder I have provided copy/paste all the contents to the inside of your Fallout 3 goty game folder. I all so provided an alternate enbseries.ini that has light exterior AO settings inside of the Light AO folder, if you notice any npc face bugs with the default one you can use the light one.

I set the Reshade Overlay key to the delete key and on the Reshade overlay I set screenshots to F12 and have the fps counter turned on, On the enb overlay the fps counter is the * key and screenshots are the Print key

Setting up the Enblocal.ini
It is important that you adapt the [MEMORY] settings in the enblocal.ini to your own hardware, the one I provided is for me and I set the AutodetectVideoMemorySize=true so it will ignore my VideoMemorySizeMb= value, but the AutodetectVideoMemorySize is said to work for some users and for other users it'll give the wrong values, it is best to use the EnbVRamSizeTest Boris provided and whatever number it gives you, subtract 2000 and place that value after VideoMemorySizeMb= and set AutodetectVideoMemorySize=false, you may or may not need to adjust other settings as well, below are some helpful links to help you do that.

Set EnableFPSLimit=false and make sure and cap your frames to 59 from your drivers

ENBLocal INI Reference

EnbVRamSizeTest

Here you can find helpful tools to test and adjust your monitor LCD monitor test images (lagom.nl)

If the enb binaries d3d9.dll causes you to crash when you launch the game then you probably need this DirectX Redist (June 2010)

Go inside your Fallout 3 goty game folder and delete the following and everything will be uninstalled

enbseries folder
reshade-shaders folder
d3d9.dll
d3d9_reshade.dll
enbhost.exe
enblocal.ini
enbseries.ini
ReShade.ini
ReShade.log
ReShadePreset.ini