In terms of ability to transfer lots of stuff quickly, firewire completely spanks usb. Just google around and you'll see some shocking data about how much faster firewire actually is. Also, I believe that due to the architecture, you take a CPU hit doing sustained transfers over usb.
Most motherboards come with USB2.0, and firewire cards arn't too expensive, so it probably doesn't actually matter what the motherboard has. However, what you need might depend on what other video equipment you're actually using.