If you have it, please go for FW800. It blows FW400 out of the water, let alone the (still) inferior USB2. On paper USB2 is faster than FW400, but don't be fooled. USB claims quite some processor power, something that FW doesn't do nearly as much. And in real world tests, it's actually slower than FW400. If it's going to be a drive for backing up to and for working on/from, please go for at least FW400. And be smart, for very little extra money, you can get a quad-interface hard drive that features both FW400 and FW800. In case you don't have FW800 now, you might have it on a future machine. Then you can use the drive to its fullest potential.
EDIT: Heed what chrono1081 wrote. Get an enclosure and an internal drive. Apart from the advantages listed above, internal drives come with a better warrenty. Often it's twice as long as for prebuilt external drives.