Oddly enough there are some software packages that won't run on a 64-bit system. I have encountered a few. Sometimes its just a matter of downloading the correct version from the vendor though.
Hardware drivers are going to be your biggest problem. If you have any old printers, scanners, or other office equipment make sure they have the drivers.
Although Vista has received a bad rap in the tech press and blogs you shouldn't discount it. Especially if you're looking at a 64-bit setup, Vista is going to have better support for hardware and software. I've been running 64-bit Vista on my primary machine for quite a while now, and it's been rock solid in terms of performance. I didn't run into any major software issues, but did have some issues with hardware drivers.