One excellent program to test and evaluate your RAM is American Megatrend's AMIDiag. They tend to fail dramatically, with lots of noise and vibration. Or the bearings that support the platter's spindle may be failing. Since a hard disk spins at up to 10,000 rpm, it doesn't take long for a bad bearing to turn your disk into metal shavings. Or maybe your drive doesn't sport such a dramatic failure, maybe it's just pausing for rest periods too often.
Occasional pauses are ok - cache flushes, accessing of swap files, etc.
Your disk's surface may be flawed, the heads may be inaccurately positioned, the electronics may have glitches, or the connections may be loose or defective. If your hard disk is doing this, you won't know it, and consequently you won't know when your disk has a problem that's causing it to recreate the bad data. PCs made after the millenium will likely store over 10 gigs of data on their inboard hard disks. A file's entry in the hierarchy can be accidentally overwritten, causing mild to major trauma to your file system. If the FAT is corrupted, your file structure may become scrambled to the point of unusuability.