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That sounds like a beast of a machine!
I encode video on my GPU a simple ATI 6970. As it has circa 1,500 processing units - it's kinda designed to handle video conversion much faster than real time.
The latest Catalyst drivers for the card come with add-ons one being the freely bundled ATI video converter (that can up and downscale as well as change most formats into every other format).
Bigasoft have a converter that might utilise your CPU more, mine isn't heavily loaded when I do conversion becuase the GPU does all the heavy lifting.
I'd be interested to know how an 40 core / 80 thread monster competes against a high end GPU. I certainly wouldn't expect it to beat a dual GPU card - or two or three operating in parallel. I'd imagine a 3 way set up of dual GPU cards (Nvidia 590 or ATI 6990) giving you 6 GPU cores running almost 9,000 threads would eat anything. I know some guys created a dual Xeon quad Nvidia GPU beastie and it does near real time tomography (3 d X-ray / MRI / CT composition of a human body). Something that a few years ago workstation level hardware took almost a day to do can be done in a little over a minute.
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