In case someone comes across this more recently, this is a well known problem and the primary fix including other performance remedies can be found in this Gopher video:
Modding Fallout 3 - Part 4 : Performance & Stability (BASIC)
However, in my experience if you want a 100% stable game you use the Tail of Two Wastelands mod to import Fallout 3 into the New Vegas engine and mod it for stability. There are simply more things you can do including using NVAC - New Vegas Anti Crash.
Currently have put ~143 hours into a play though and I might have had one or two crashes? Regardless I can't remember the last time I did have a CTD. The only problem I have ran into is after about 6 or 7 hours the game gets slower and starts to chug in which case you just restart it.