Improving disk throughput usually translates -> new hardware. You can try a different file system or block size. XFS for Linux is improving. You may want to compare it to ReiserFS. If you are going to test different block sizes for the db, partition accordingly with the db on a separate partition from the OS, Apache, PHP and MySQL binaries. This way, you can leave the binary partitions at a smaller block size and adjust the db partition without affecting the others. When installing your db on a second machine do the same; isolate your binaries from your data.
I'm sure I'll end up doing some of that. Right now, I'm using an old Compaq with a small (8Gb) disk for the test installation, mainly because it's trashable. But the software is relatively stable and safe now, so I'll install it on my main development box with the nice 10,000 RPM SCSI and a gig of ram, and run the test suite from the Compaq instead.
I'm a big fan of ReiserFS in general. That's what the MySQL folks recommend as well, and I run that at Piclab (which is a small machine but runs the testsuite faster than my Compaq). I'm not sure that block sizes are that flexible for Resier, but I'll look into it. At any rate, it would be good to find an optimal arrangement for the database before we get the new server to install it on.