See if the bar progresses. If not, hold the Power button to turn off your computer and turn it on again. If the update wasn't installed, install OS X 10.8.4 with the Combo edition > http://support.apple.com/kb/DL1659
If you can't start up Mac OS X, hold Command and R keys while your Mac Pro is starting and reinstall Mac OS X. You won't lose any file
If you have it backed up then I would kill it. If you don't and the update is still progressing then leave it alone. Most likely it's taking a while because the system you are updating was dysfunctional.
If you stop it and are still able to boot the computer then do the following:
Repair the Hard Drive and Permissions - Lion/Mountain Lion
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported then click on the Repair Permissions button. When the process is completed, then quit DU and return to the main menu. Select Restart from the Apple menu.
After this is completed download and install OS X Mountain Lion Update v10.8.4 (Combo).
I did a shut down and machine restarted under 10.8.3
When I went to software update, it looked like it would not work, but it finally went straight to "needs to restart" and installed the software without a new download.
I am now running 10.8.4 and all appears to be working as expected.
I ran permissions repair and was amazed that there were no listed items repaired with over 900,00 files on the primary drive.
(sure don't need this kind of stress at 1:30 am after a long day)