Howdy. I tried getting an eVGA 8800GT going on my mac pro with no luck. I think it certainly can be done, but I really do suspect some firmware editing could be necessary. I did get my hands on an apple video card power cable from a local apple repair centre. That seemed to be a very necessary component. However I couldn't actually get the machine to boot up with the eVGA card.
Still, if I had the $, I'd go get one and try it again, using more of the switching back and forth techniques discussed earlier in this thread. At the end of the day I'm currently running Ubuntu on my Mac Pro more than anything, so I'd really like to be a bit more open to switching up some hardware.
I love being able to use OSX, but with the recent leaps with osx86 I doubt I'll ever buy another mac pro. They make beautiful hardware that I'm happy to pay for, but their tight-ass insanity over maintaining control of their brand makes me keep them at arms length. That said, I'll keep buying macbooks for quite some time to come as long as I can continue to change the typical stuff - memory/storage.