@peterdrake Failing drive then? smartctl --all /dev/hda (or similar drive path), could provide some details.
If the drive is getting old and is starting to fail, that can result in slow head scan times. Smart can provide you with some internal metrics about the drive.
Another issue I've ran into is swapping. If your OS is trying to copy memory over to swap, that will also hinder system performance.
sudo iotop, top, and the System Monitor GUI application can provide some hints about what's using resources.