If you're only ever going to plug it into that one system, there's not going to be a big difference. WinXP, certainly, (and 2k, too, but I have less experience there) supports FireWire in basically the same way it supports USB. For standard things (hard drives, CDROMs, etc.), there should be no additional config, but you mgiht want to check with the manufacturer to make sure they haven't done something wonky. I have this notion that FireWire hubs are going to be more expensive than USB2 hubs, but I could be wrong.

If you want to plug it into other things, there are differences. USB2 is a lot more common than FireWire these days, especially considering that it can work as USB1 as well. But FireWire doesn't have the host/device idea. You can plug host into host and device into device with no problems. (Of course, taking advantage of that may not be as easy.)

Also, note that the original FireWire spec is about the same speed as USB2. (Technically, it's 400Mbps for FW and 480 for USB2, but the greater overhead in USB seems to virtually negate that difference.) FireWire 800 is available and is twice as fast. That might be a consideration for later on.