I'm currently going through a ton of crashes, trying to figure out what's wrong before I can even continue.
I couldn't resist and installed my FO3 GOTY again, got TONS of mods and the game kept crashing every 10 minutes or so, randomly. That's why I stopped playing Oblivion, I wanted to play it so badly with all the different mods (FCOM mainly), but all I did was that instead of playing the damn game, I was solving problems. With FO3 it's kinda the same, except I found a way to minimize the crashes a bit. I used FO3Edit's master update function, play in windowed mode and http://www.pdsys.org/blog/post/2009/02/07/Fallout-3-VideoDisplay-Freezes-sound-keeps-going.aspx. The crashes are minimal now but there are other problems...
EDIT: http://www.tomshardware.co.uk/forum/page-100562_25_50.html. It MIGHT help.