Have you been installing a lot of mods? If so, you could try deactivating them one at a time to see of one is having a big impact on performance. Check out how many processes you have running in the background as well.
http://www.tweakguides.com/Fallout3_1.html The tweaking guide linked on the second page is also amazing for optimizing your system in general. It can take a while to go through, but there is some very good advice.