I know a lot of people say use FOOK2, however I have found Fallout Mod Manager to be very usefull and a good number of mods out there are made for it.
Fallout Mod manager [FOMM] http://www.fallout3nexus.com/downloads/file.php?id=640
Bunker 72 Housing Mod, a very cool housing mod http://www.fallout3nexus.com/downloads/file.php?id=7455
Fallout 3 Re-Animated, changes and improves how you carry and use your weapon http://www.fallout3nexus.com/downloads/file.php?id=7670
I would suggest playing threw with the current set of weapons before getting weapon mods because many of them really dull the game out. What challenge is there when you can fire one shot from a pistol and drop a behemoth after hitting its leg?
Also keep an eye out for mods made by Crowbennett08 on Fallout 3 Nexus, they seem to be the better ones from my personal experiance, and a few other mod makers have given him shout outs for helping them in some way.