heh, Oops! comp freezing

I was running spysweeper the other day and it had me
manually delete some of the files it could not, I think i
might have incorrectly deleted some important files.
My computer now tries to load up but hangs at the
welcome screen, thus safe mode and system restore are not
available to me. Chkdisk can find any errors (not sure if
it should). Are there any great minds with some
suggestions on what I should do? I dont really want to
reformat as i want to keep all my settings and apps.
thanks, Mike