Defrag, optimal* swap file size, not running low on disk space, service packs up to level. Aside from those, check which processes are using cpu cycles, anything that stands out trace it to the app calling that process.

Activate the diskperf service and the examine the performance monitor, details [link|http://support.microsoft.com/default.aspx?scid=http://support.microsoft.com:80/support/kb/articles/q102/0/20.asp&NoWebContent=1|here]


*many arguments as to how large/small the swap file should be in relation to amount of memory- My rule of thumb is twice the size of RAM.