This thread aims to be a comprehensive list of known Fallout 3 modifications.
If you post an announcement in this thread and/or send me a PM, your mod will be added to the following list - complete with website-links, download-links, and a small description.
Any releases/status changes should be brought to my attention by PM, or posting in this thread.
Please refrain from discussing modifications in depth here, however, as that would mean this thread would get way too cluttered.
No Magical Enchantments on Armor: Removes all of the magical enchants on items (i.e. 1 Luck, +1 PER, +5 Science, etc). The only armors not altered are the Lucky Shades and ALL Power Armors. [Download]
Big Guns Strength Requirements: This mod adds minimum strength requirements to all Big Guns (>=7) [Download]
Realism test: Mod for added realism. Modifications are as of now relatively limited, for lack of CS. [Download]
Remove Bobblehead effects: Removes the effects that the bobbleheads in Fallout 3 give. Does not work retroactively, but will work with any saved game. [Download]
Level Cap Increaser: Increases your level cap to 30 or 40. BEWARE: if all your skills are maxed, you might get stuck in the leveling screen. If this happens, enter the console and type "closeallmenus" to continue playing. [Download at link]
No God mode VATS: Makes the player take damage in VATS, and can optionally reduce the amount of damage player does to enemies in VATS. Values can be changed from 50% up to 200%.
Weight mod: Rebalances the carried weight system in the game. Makes it so that higher strength will enable to you carry more than the vanilla game (with 10 Str you can carry op to 350); and that low Str characters will not be able to carry as much as in vanilla. [Download]
Slower Item Degradation: Reduces the rate at which items degrade. You can choose between 50% and 70%. [Download at link]
Unique Zhu-Rong v418 Pistol: Custom skin for the unique Zhu-Rong Chinese pistol. [Download]
Medicine and edibles Revamp v.0.2: Remakes the drugs so that their effects in Fallout 3 are similiar to those in previous Fallout games.[Download]
Fatman Thermobaric Warhead: Replaces the Fatman mini-nuke with a thermobaric warhead. [Download]
AA-112 Combat Shotgun: This mod modifies "The Terrible Shotgun" (unique combat shotgun) into the AA-12, a fully automatic shotgun. [Download]
Valhalla Rifle: Adds a new weapon in game (doesn't replace anything). WIP. [Download]
Interface & HUD
Vista console fix: Fix for users having trouble using the console in Vista. [Download]
Pipware UI: Combines CND and RAD Pages, with faster access to the EFF Page.
Lists are easier to traverse with a less thin Scroll Marker, and the option to jump 1 Page of items instead of 1 line when using the mousewheel.
Also has some slightly improved screen-space usage for menus and dialogs. [Download] 
Fallout 3 Item Descriptions: Adds Item descriptions to the game! [Download]
MTUI Mod: Essential UI adjustments for Fallout 3: smaller fonts, larger item selection areas, improved conversation menus, etc. Designed for screen resolutions of 1024x768 and higher. [Download]
Larger Dialogue Boxes: Increases the size of the dialogue boxes, while leaving the size of the fonts the same. Greatly reduces scrolling. [Download at link]
Radation Redux: Removes radiation level feedback, as in the original games. Radiation level and effects are no longer displayed. [Download] 
Minimal UI Mod 4: Scales down interface, and uses original Fallout fonts. [Download]
Minimal UI 4 + Revelation: A combination of the Minimal UI Mod (see above) and the Revelation mod (which uses menu textures from Fallout Tactics and Aquanox 2: Revelation). [Download] 
No Waypoints and Markers of Any Kind Mod: Small mod that ensures the compass doesn't tell you where to go all the time. [Download] 
Remove Compass POI Markers: Removes all Place of Interest and Quest markers [download at link]
Remove waypoints and NPC info from compass : Does what it says. [download at link]
High Definition Texture Pack: A player-created compilation of many High-resolution textures for Fallout 3. It vastly improves the visuals of Fallout 3 without changing the overall "Fallout 3 look". [Download]
Mimezu's Texture Pack + addons: Superiour textures for the 'blurry' ones in the vanilla game. (single file, includes texture pack and three addons) [Download] 
T-51B as default BoS power armor: Switches textures so the default PA is T-51B. [Download] 
Original Combat Armour: Re-texture of the Combat Armour to more closely resemble the originals. [Download]
Higher Res Blood decal: Makes blood & gore look better - but does not change the amount of gore overall.
10mm Nexus Handgun: Better textures for the 10mm handgun.
Millenia's assorted works: User-made textures.
Vault Music Mod: New music for vault/underground bunker environments. See link for installation details. [Download]
Fallout 3 Classic Music Mod: Fallout 1&2 background music for FO3. [Download]
An Ultimate Fallout 3 Music Mod: An easy set to import Fallout 1/2 music to Fallout 3 [Download] 
Public's music MOD (Tribal Ambient): Public claims to be working on a music mod. Is he speaking the truth? Or does he just want his name up here? Only time will tell.
Realistic Gun Sounds: Changes the sounds of most conventional firearms to be more realistic. [download at link]
No Bad Karma Noise: Removes the sound that plays when you gain negative Karma. [Download at link]
Remove UI Sounds: Removes many sounds, most notably the cash-register sound when you gain XP. [Download at link]
Character Editor: Ayeso's Character Editor
Mod Manager: A Fallout 3 mod manager/switcher
Fallout 3 Savegame Manager (F3SgM): Savegame manager. See this wiki link for further info.
FOMM: For extracting files from the .bsa archives, and can open Fallout3.esm, as well as craft new .esp files. [Download]