Assume you have done the whole virus/malware scan thing. Is everything ok under the device manager, no exclamation marks? Plenty of hard drive space left? Once booted is it working at a normal speed? Could try something like Sisoft Sandra to benchmark your hard drive (smaller utilities exist, can't think off the top of my head). If the desktop is appearing reasonably quickly but taking forever to settle are there lots of things in the startup?
Any reason why you are sticking with service pack 2? Installing service pack 3 may update some system files that are causing problems.
Could be a bunch of things really. I'd be tempted to benchmark the hard drive first though. Most of the utilities will show a graph as they go along which might give an indication. Actually most hard drive makers have little utilities for drive diagnostics to download, make sure there are no problems building there!