Over the weekend I realized that my notebook became quite slow and was always reading something on the HD, even without any memory pressure. When I was to some music, starting an application was really corrupting the sound. So after some I realized that my Primary IDE controller went from DMA back to the old PIO mode. To solve this issue I reinstalled the the primary IDE port using the Device Manager, and after two reboots it went back to DMA and a acceptable speed.
You might find more information about that issue here: IDE ATA and ATAPI disks use PIO mode after multiple time-out or CRC errors occur.