Another issue that can make a computer slow, is if the ATA controllers have kicked down to PIO mode. This forces the CPU to spoon-feed EVARYTHING to/from the hard drive.
To check whether that happened,
1) log on as a Computer Administrator, right-click My Computer > Properties, then click the Hardware tab and open Device Manager
2) go down to the IDE ATA/ATAPI controllers and click the "+" to expand it. There will be multiple controllers listed.
3) for each controller, double-click it to open its panel, then go to the Advanced tab and make sure nothing's in PIO mode. If anything IS in PIO mode, then click the
Driver tab for that controller, and click the
Uninstall button. This makes Windows rediscover the controller and give it another chance at using DMA modes.
Also, as a second and third opinion, use these online antivirus/antispyware/antirootkit scanners (use Internet Explorer for these scanners, since they're ActiveX-based):
F-Secure online scanner
Microsoft OneCare online scanner
You'd be surprised how much stuff one antivirus product can miss. So run these other ones and increase your certainty about it being clean. Like
Lemon law said, posting your HijackThis log is another good idea.