Hmmm, nobody answered yet?
See if the Disk is issuing any S.M.A.R.T errors in Disk Utility...
Open Activity Monitor in Applications>Utilities, select All Processes & sort on CPU%, any indications there?
How much RAM & free space do you have also, click on the Memory & Disk Usage Tabs.
Open Console in Utilities & see if there are any clues or repeating messages when this happens.
In the Memory tab of Activity Monitor, are there a lot of Pageouts?