I ususally run Fprot, MS Antispyware, and Zone Labs..
If you have a potential virus, run those (all)
Spybot : http://www.download.com/3000-8022-10122137.html
adaware : http://www.lavasoftusa.com/
STINGER : http://vil.nai.com/vil/stinger/
http://housecall.trendmicro.com/ online scan for trojans
http://www.ravantivirus.com/scan/
http://www.spychecker.com/program/coolwebshredder.html CWshredder
http://www.spychecker.com/program/hijackthis.html download
http://www.hijackthis.de/index.php?langselect=english check the log
if this is not the cause, you can look for big files and folders, they can slow down your system; eg a zip file of 4Gb could cause this; so check the folders and delete the temp folders