i just got my MacPro today. It beeps too. i first heard the beep when i turned the system on and then found that my superdrives did not work... this was becasue i had installed another one when the machine arrived and failed to set the new Superdrive to cable select.
i took the beep to be indicating that something was amiss with the system, and sure enough it was. Easy enough to fix, however.
Then, just now, i heard it beep again, this time i have no clue as to why. i came on here to see if anyone else knew... As it is, i am thinking the beeping indicates some sort of error or other.