I know that this isn't a cure all solution, but you can try running the http://www.fallout3nexus.com/downloads/file.php?id=6510 on your Fallout3.exe.
Follow the directions in the readme to the letter! Especially, make a backup copy of Fallout3.exe. Go to your Fallout3 install folder, right click on the file, and select Copy. Then right click a blank area in the folder, and select Paste. You'll get a file named Fallout3 - Copy.exe.
The LAAE reduced my CTDs alot. I hope it works for you, too.
Good luck.