Quite a few people have experienced Vista disk thrashing at intervals. There can be multiple reasons for this, as Microsoft has tried to be very thorough with security and enables, by default, the following:

• Index build for faster search: if you don’t search your computer for files every other day, might be a good idea to disable it. Runs in low priority.
• Drive defragmenting is typically scheduled once a week, set to Wednesday evening by default on my machine. Runs in normal priority, can effectively make your computer grind to a halt. Either set an idle date when you’re not at your desk to run it, or disable it and run the defragmenting manually.
• System restore points also run at intervals, typically when you’ve just installed a new piece of software. Best keep that going, it’s a nuisance at times but can save you a lot of trouble later on.