I thought, logically, that it was a hard drive problem. I pulled all the drives, put in a new one and reinstalled Lion from an external drive
However, the clicking was still there. So I tried pulling the new drive and rebooting with only the external Firewire drive connected (it has an SSD in it, so no moving parts) and it still made a clicking sound without any drives attached
What else in a MacPro could cause the clicking sound and a reboot to hang?