One of our development boxes has developed a problem wherein performance will occasionally drop through the floor. When this happens, you can hear the hard drive thrashing, but I don't know what's causing it.
This happens during periods of high disk access (reading/writing multi-gigabyte files), but not every time nor for the entire period of disk access. Those files are also kept rigorously defragmented specifically to prevent the kind of "seek thrashing" that seems to be occurring.
I suspect that the problem lies either with the system's antivirus or with some disk-indexing service I don't know about (AFAIK, there aren't any running, but…). Unfortunately, my Performance Monitor-fu is very, very weak (okay, nearly non-existent), and I don't know how to confirm/disprove my suspicions or find out what the real culprit is.
Process Explorer located the culprits for me — the Java Quick Starter and Windows Search services. Turning off the former had a noticeable impact on performance and turning off the latter had an enormous one (despite having not been given any files to access). Both were performing 5-20 times as much disk access as any other process.
Thanks all for your help!