When writing about my encrypted disk partitions, I noted that “the drop in performance [with IDE] is definitely noticeable [compared to SCSI]... any disk-intensive activity also drives up the CPU load.”
Well, it turns out that my kernel was configured incorrectly, leading to extremely poor IDE performance. Some investigation with hdparm revealed that DMA (direct memory access) was not enabled! No wonder it was so horrible. What's worse, hdparm is unable to turn it on with my custom kernel. So I booted an Ubuntu stock kernel, and DMA was enabled automatically and read throughput was about 7 or 8 times faster. Wow, all this time I thought IDE just really sucked that bad!
So now I need to figure out what's wrong with my custom kernel. True, I did build it back when I was primarily using SCSI – I think the only IDE drive I had in this machine at that time was for Windows 98.