|It depends what kind of system restore you run. If you do a standard restore, it shouldn't lose any programs that you've purchased.|
A good place to start is with the Windows Startup options. Disabling programs you never use there will make things run a lot faster.
I'm not quite sure what you mean with the documents folder problem though. More than one folder as in a copy of the original...?
If Vista is that messed up, it's probably going to be easier for you to do a restore.