Beirut, have you spent some quality time in msconfig? That usually helps me when I'm getting weird slowdowns ...

Also, when you give the three-fingered salute, the CPU usage should start in the low single digits and quickly drop to zero. (It starts showing usage because you're summoning the Windows Task Manager; once that's fully loaded your CPU monitor should drop to nothing.)

Another possibility: check your disk usage. If you've got, say, a 60-gig drive and it's got 59 gigs of stuff on it, performance is gonna suuuuuuuuck. You should always have a few gigs free on the HD for the pagefile and other such necessities.