Sorry.
Short of reinstalling, you can do something of a reset...move everything besides the vanilla FS2 VPs, the launcher, and the exes, to a different directory. (It might be easier to move the aforementioned to a new directory, and rename the folders so the new one is the same as the old Freespace 2 directory)
At that point, check the registry keys and make sure nothing's amiss (maybe post a screenshot of 'em in the forums and ask if you're not comfortable with registry editing) then run FS2. Everything should be generated from scratch, and you can move mods and stuff back in as you want them. Once FS2 stops working again, you can figure out what caused the problem.
