That's the second HD I've had go "bad" in the past two weeks. This time it was in my linux box and I had more opportunity to diagnose it. I couldn't see any of the files/directories that were on the disk, even though it was mounted just fine. All the paritions in fdisk seemed normal, and even a reboot didn't help. I was unable to unmount the drive because it complained that the device was in use.

I was very worried that I'd lost 200 gigs worth of data. Rebooting did tell me that S.M.A.R.T was malfunctioning, and so did smartctl. I loaded up the Ultimate Boot CD again and did the IBM HD check and it found no errors. One reboot later the S.M.A.R.T errors had gone away and all my data is back. Malfunctioning S.M.A.R.T must cause the OS to stop seeing the data on the disk. Luckily for me it was a semi-easy fix.