Below is material from the dark ages before the Apple fix - so relevant to Leopard users only.
One possible fix is to use a PCIe sound card such as the ESI Maya 44e (~$150, probably the cheapest) or other PCIe audio cards. These seem to avoid the bug being evoked when playing sound. NB. other sound devices connected by Firewire or USB will evoke (rather than prevent) the bug.
Apparently using AirTunes speakers can prevent the bug being evoked.
If there is no need to use any audio or copy Firewire drives, the bug should be a non issue for you. Just make sure you have not installed any audio devices which evoke the bug.
Reassurance: try SMC reset.
Some advocate just living with the performance loss and electrical power wastage, and if overheating the CPU causes failure - just get a repair on AppleCare. There are a few negatives to this approach: not green, why pay a premium for a slowed machine, but chiefly AppleCare seem unlikely to offer replacement machines, are slow (expect 3 weeks turnaround), expensive, uncommunicative, offer no stand in loan machines and can be extremely frustrating to deal with.
If Apple produces a fix, hopefully available (not at time of writing) at: http://support.apple.com/downloads/#macpro
(the current patch only works under Snow Leopard, and the Mac Pro EFI Firmware Update 1.3 has no effect
on the bug)