I have a Mac Pro, 2.8 GHz, quad-core Intel Xeon, 4 core machine. Two weeks ago, my second internal HD disappeared. That morning the computer was making clicking sounds when I booted up - it still does. Also, when the computer comes back up from sleep mode, it clicks. What can I do to fix this?
Sounds (Ha!) like a bad hard drive. Have it replaced.
You can try using something like Diskwarrior to repair the file-system, but it is highly unlikely that will work if the drive is making odd sounds.