wow.
just off the top of my head:
http://fallout3nexus.com/downloads/file.php?id=640
FOMM. mod manager. you'll need it.
http://fallout3nexus.com/downloads/file.php?id=944
makes invalidating archives (for texture swaps / add-ins) a snap.
http://www.bethsoft.com/bgsforums/index.php?showtopic=949858&hl=darnified
a MUST have. does some very needed things with FO3's console-UI.
http://www.bethsoft.com/bgsforums/index.php?showtopic=951381
fallout 3 script extender. a lot of the more complex (script based or triggered) mods will need it.
http://www.bethsoft.com/bgsforums/index.php?showtopic=962670
modified rules, game dynamics and combat modifiers. clever work.
http://www.bethsoft.com/bgsforums/index.php?showtopic=958148
revamped from top to bottom, leveling changes, loot changes, too much to list here.
http://www.bethsoft.com/bgsforums/index.php?showtopic=961325
an insanely amazing crapload of guns. a LOT of guns. seriously.
http://fallout3nexus.com/downloads/file.php?id=1784
being born was bad enough the first time. skip it.
http://fallout3nexus.com/downloads/file.php?id=774
the best texture packs out so far?
http://fallout3nexus.com/downloads/file.php?id=1516
if you killed them, why cant you keep their stuff?
http://fallout3nexus.com/downloads/file.php?id=1409
ridiculously awesome perks. also more in the spirit of fallout canon.
there's a lot more, tho.
seriously, this reply could be ten pages long.
http://www.bethsoft.com/bgsforums/index.php?showtopic=962509
i liked that one. just added another little touch of immersion in regards to the BoS.
http://www.bethsoft.com/bgsforums/index.php?showtopic=959952
i keep an eye on that one, because the amount of "shell" buildings in fallout3 is large.
http://www.bethsoft.com/bgsforums/index.php?showtopic=956936
allows most small arms weapons to be upgraded with silencers, extended magazines, scopes, etc...