Most folks are in the 32-bit camp, with good reason. Ultimately, however, your hardware and software configuration should be the major deciding factor, IMHO. If you run a fair amount of older and/or non-MS software, or you have and want to use bluetooth keyboard/mouse, then 32 bit is definitely the right choice. If you primarily run newer versions and/or mostly use MS software (Office and the like), then 64 bit may be a good choice for you.
I started out by running XP on my Mac Pro, and when Vista came out I upgraded to 32 bit Vista. Total disaster. I had to add memory to my Mac Pro to have usable video (for reasons I never understood, you need at least 2GB of main memory). After that was addressed, I found it was completely unstable; it would crash just opening IE. So much for doing an upgrade.
After much consideration, I did a clean install of Vista 64 bit. Everything except the audio came up right away (note: you can't use the bootcamp drivers at all since they are all 32 bit). The 64-bit audio drivers are available at Realtek's website. Bluetooth doesn't work, since those drivers come on the bootcamp drivers disk (so I reverted to a USB keyboard and an MS USB wireless mouse). 64 bit is both more secure and more stable than the 32 bit version, in my experience. I've been using it ever since (four months now).
There is one other issue that may be bothersome; the time delta between MacOS and Vista is normally addressed with software loaded on the bootcamp drivers disk. I've never successfully gotten that to work by loading it manually, so I just manually do a time update once I boot into the opposite OS.
In terms of compatibility, the only issue I ran across was when I recently acquired "Star Wars: The Best of PC", which includes 5 games. Two of the older games (KOTOR and JKII:Jedi Outcast) simply wouldn't run (though I didn't attempt some of the compatibility tricks you can try). Conversely, StarCraft (a very old game) runs just great.
The only other downside I can think of is that it appears Apple has no intention of supporting 64 bit with bootcamp. Not sure if that's because there are so few people running it, or because they don't want people to see MS has actually built a decent OS. ;-)