Just posting it here for people who might have the same issue.
The game engine has some issues with processors that have more than 2 cores. You can force the game to only use two of them and it will stop the freezing. I haven't had it freeze once since I did this several days ago.
Open up the fallout.ini file in: My Documents\My Games\Fallout3
Find the line:
bUseThreadedAI=0
change it to:
bUseThreadedAI=1
Add another line after it and insert:
iNumHWThreads=2
This will limit the game to 2 cores and prevent the engine bug from causing the game to freeze.
