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Don't forget to check out Ledsen's Oblivion modding thread too!
New and Improved (updated 18/01/2012)
Welcome to the new and improved mods thread for the 3D Fallout games. The original OPs focused a lot on how to actually install mods, but I'm going to keep that down to a bare minimum this time around since there's already a lot of tutorials online about how to get started.
N.B.: Most screenshots are taken from the original mod pages and were supplied by users of the mods, or the creator themselves. If you're either of those people and want the image(s) removed or attributed please send me a PM.
The Checklist
Before you start modding, run through this checklist:
If you answered "yes" to all of the above, it's time to start modding.
Graphics
Project Beauty

Project Beauty replaces every single NPC face in the game with one which has avoided the ugly-stick.
http://www.fallout3nexus.com/downloads/file.php?id=6341
Fellout
Fellout brings green grass and blue skies back to the wasteland.
http://www.fallout3nexus.com/downloads/file.php?id=2672
NMC’s Texture Pack

Inspired by Qarl’s amazing work on Oblivion, this mod replaces every single texture in the vanilla wasteland with a photographic image-map 200 - 400% larger than the original.
http://www.fallout3nexus.com/downloads/file.php?id=12056
Gameplay
DC Interiors Project
The DC Interiors Project adds a huge number of indoor locations to the game, some of which span multiple instanced areas and have mini-objectives.
http://www.fallout3nexus.com/downloads/file.php?id=5573
Mart’s Mutant Mod
This is the quintessential overhaul mod. The aim is to make the game a lot harder right from the start, and it delivers.
http://www.fallout3nexus.com/downloads/file.php?id=3211
Fallout: Wanderer’s Edition
Basically the greatest mod ever made for anything, Wanderer's Edition turns Fallout 3 into S.T.A.L.K.E.R.: Shadow of the Capitol.
http://sites.google.com/site/fo3wanderersedition/
RH Ironsights
Ironsights in Fallout 3. And they actually work! Combine this with Wanderer's Edition for the real survival FPSRPG experience.
http://www.fallout3nexus.com/downloads/file.php?id=6938
RTS: Realtime Settler
A complete change of pace from most gameplay mods for Fallout 3 which aim to improve the action with better combat mechanics, the RTS mod brings Sim-City to the Capitol Wastes.
http://www.fallout3nexus.com/downloads/file.php?id=7070
Interface
Darnified UI
High-resolution fixes for the UI in Fallout 3. Also changes the default UI font to something I hate, so I don't use this.
http://modsreloaded.com/darnified-ui-f3
MTUI
Nothing but fixes for higher-resolution, I much prefer this to Darnified.
http://www.fallout3nexus.com/downloads/file.php?id=43
aHud
Allows you to move almost any HUD element around to a new location, as well as remove the brackets around them.
http://www.fallout3nexus.com/downloads/file.php?id=15886
Crosshair (?)
I'm not going to recommend a particular crosshair as they're all pretty much interchangeable. If you want somewhere to start, I use a mod with the imaginative name 3 new Cool crosshairs:
http://www.fallout3nexus.com/downloads/file.php?id=7603
Miscellaneous
Maximised Window
This little mod will wait a few seconds after the game launches and then forcibly maximise the window.
http://www.fallout3nexus.com/downloads/file.php?id=45
Games for Windows Live Disabler
Kill it with fire.
http://www.fallout3nexus.com/downloads/file.php?id=1086
Troubleshooting
Mods can mess with one another pretty seriously, and it can often be hard to work out which combination of mods is causing you to crash to desktop every few minutes. Thankfully a lot of the major conflicts have been identified and fixes for them have been rolled into Fallout Interoperability Project (FOIP) packages.
FOIP: http://www.fallout3nexus.com/downloads/file.php?id=4968
New and Improved (updated 18/01/2012)
Welcome to the new and improved mods thread for the 3D Fallout games. The original OPs focused a lot on how to actually install mods, but I'm going to keep that down to a bare minimum this time around since there's already a lot of tutorials online about how to get started.
N.B.: Most screenshots are taken from the original mod pages and were supplied by users of the mods, or the creator themselves. If you're either of those people and want the image(s) removed or attributed please send me a PM.
The Checklist
Before you start modding, run through this checklist:
- Have I backed up my game install?
- Have I installed Fallout Mod Manager?
- Have I installed Fallout/New Vegas Script Extender?
- Have I installed 7zip and WinRAR?
- Have I registered for an account on The Nexus Forums?
If you answered "yes" to all of the above, it's time to start modding.

Graphics
Project Beauty



Project Beauty replaces every single NPC face in the game with one which has avoided the ugly-stick.
http://www.fallout3nexus.com/downloads/file.php?id=6341
Fellout



Fellout brings green grass and blue skies back to the wasteland.
http://www.fallout3nexus.com/downloads/file.php?id=2672
NMC’s Texture Pack



Inspired by Qarl’s amazing work on Oblivion, this mod replaces every single texture in the vanilla wasteland with a photographic image-map 200 - 400% larger than the original.
http://www.fallout3nexus.com/downloads/file.php?id=12056
Gameplay
DC Interiors Project



The DC Interiors Project adds a huge number of indoor locations to the game, some of which span multiple instanced areas and have mini-objectives.
http://www.fallout3nexus.com/downloads/file.php?id=5573
Mart’s Mutant Mod



This is the quintessential overhaul mod. The aim is to make the game a lot harder right from the start, and it delivers.
http://www.fallout3nexus.com/downloads/file.php?id=3211
Fallout: Wanderer’s Edition



Basically the greatest mod ever made for anything, Wanderer's Edition turns Fallout 3 into S.T.A.L.K.E.R.: Shadow of the Capitol.
http://sites.google.com/site/fo3wanderersedition/
RH Ironsights



Ironsights in Fallout 3. And they actually work! Combine this with Wanderer's Edition for the real survival FPSRPG experience.
http://www.fallout3nexus.com/downloads/file.php?id=6938
RTS: Realtime Settler



A complete change of pace from most gameplay mods for Fallout 3 which aim to improve the action with better combat mechanics, the RTS mod brings Sim-City to the Capitol Wastes.
http://www.fallout3nexus.com/downloads/file.php?id=7070
Interface
Darnified UI



High-resolution fixes for the UI in Fallout 3. Also changes the default UI font to something I hate, so I don't use this.
http://modsreloaded.com/darnified-ui-f3
MTUI



Nothing but fixes for higher-resolution, I much prefer this to Darnified.
http://www.fallout3nexus.com/downloads/file.php?id=43
aHud
Allows you to move almost any HUD element around to a new location, as well as remove the brackets around them.
http://www.fallout3nexus.com/downloads/file.php?id=15886
Crosshair (?)
I'm not going to recommend a particular crosshair as they're all pretty much interchangeable. If you want somewhere to start, I use a mod with the imaginative name 3 new Cool crosshairs:
http://www.fallout3nexus.com/downloads/file.php?id=7603
Miscellaneous
Maximised Window
This little mod will wait a few seconds after the game launches and then forcibly maximise the window.
http://www.fallout3nexus.com/downloads/file.php?id=45
Games for Windows Live Disabler
Kill it with fire.
http://www.fallout3nexus.com/downloads/file.php?id=1086
Troubleshooting
Mods can mess with one another pretty seriously, and it can often be hard to work out which combination of mods is causing you to crash to desktop every few minutes. Thankfully a lot of the major conflicts have been identified and fixes for them have been rolled into Fallout Interoperability Project (FOIP) packages.
FOIP: http://www.fallout3nexus.com/downloads/file.php?id=4968