Well assuming you do not have a recent backup to fall back on, you don't have much to lose by attempting to reinstall the OS X Server 10.6.8 combo updater. Restore from backup would be my first choice, but if not you could try the reinstall. Not many options beyond that which I am aware of. See if you can do the reinstall in Safe Boot mode, else boot from an external drive and point it at your server.
No answers in this reply, just questions....
By "not helping" (sorry for my being dense here...), do you mean that safe boot doesn't work at all, or that it produced incorrect results. Similarly, do you mean that there are no errors logged by the disk repair operations, that there are errors that are resolved, or that there are errors not being resolved? If there are diagnostics from these, what are the details of the errors?
Any external or third-party devices involved here? Test: disconnect all external hardware except the keyboard, mouse and monitor.
Any RAID controller(s) involved?
Do the hardware diagnostics report any errors?
Any third-party devices installed within the Mac Pro system?
Anything in the startup logs? (Might have to use target disk mode to get at those...)
WAG: Tried resetting the SMC?
As Don Roedl mentions, you may be in line for a reinstallation here.