I had reason to copy my harddrive off and back (to reformat as case-sensitive), and I missed one very important detail.
IMPORTANT STEP: disable "Ignore ownership on this volume".
Yeah, with everything owned by user 99, it won't even boot. You can boot into single-user mode and "chown -R root:wheel /" which will at least let it boot, then you can go into Disk Utility and repair permissions (which will actually do something useful and vital in this situation). Then chown -R your home directory. But it's still a mess to clean up, and you lose all that user and group info.