I recently discovered the following while trying to get my Mac Mini to boot from a FireWire drive.
I'm a recent switcher. I took some leftover PC parts I had, and combined them with a Mac Mini to make a pretty decent machine. One of those pieces was a 160GB hard drive originally used in a Windows machine. I popped the drive into a FireWire enclosure and connected it to the Mini. I formatted it as Mac OS X Extended (Journaled), and stored media on it for a while with no problems. When I got tired of my slow internal drive, I decided to run the system entirely from the FireWire drive.
I used Carbon Copy Cloner (CCC) to clone my existing installation to the FireWire drive and rebooted, but I couldn't for the life of me get OS X to boot from the drive! I then formatted a very old hard drive and CCC'ed a clean OS X installation onto it, and it was able to boot. After some sleuthing, I figured out the problem:
Mac OS X Hints
http://hints.macworld.com/article.php?story=2006012708233610