Check the drive for errors. This is how:http://windows.microsoft.com/en-US/windows7/Check-a-drive-for-errors
If it's not the hard drive, maybe some processor-heavy background process kicks in from time to time, which you can monitor in Task Manager:http://windows.microsoft.com/en-US/windows7/Open-Task-Manager
On processes tab, be sure to click show all processes, and order the table by CPU usage by clicking on the table column header.
You can also add additional columns (menu item "View->Select Columns"), e.g. I like to add I/O columns to see, what processes make many disk operations.