Do I install 32-bit or 64-bit versions of Windows on new Mac Pro?

You'll be a lot better off with the 32 bit version. It's a lot more compatible with programs.

Apple doesn't offer 64 bit drivers yet and probably won't until Leopard comes out. I put the 64 bit Vista on my macbook pro and had to go hunt for drivers(not so easy) and certain apple specific hardware I could not find drivers for. Then again the components in your computer aren't as Apple specific as the notebooks (such as the keyboard backlight, screen brightness, "fn" keys, iSight, etc.. none of which worked with 64-bit vista)

Stick with 32-bit as noted above. You'll be happier... Unless you plan on working with HD images/video you most likely won't need 64-bit. 32-bit, however, won't be able to take advantage of more than 3GB of ram (I believe).

Until more Windows-based software takes advantage of 64-bit your safer to stay with 32-bit.

There is little justification to go with 64 bit in any case except for the ability to access more than 2GB of RAM in Vista. 64 bit is only 10% faster overall, and virtually all of this is due to floating point calculations.