Personally I'd say USB, as parallel ports are gradually becoming rarer, and can be quite tempremental to setup.

I run a Smoothstepper, and would recommend it, however development does seem to be very sporadic. I stopped paying much attention to the Warp9 forums, but I do know Greg was looking to develop a network based Smoothstepper once he'd ironed out the remaining bugs in the existing SS.
There are other options, such as thr Dynomotion Kflop, but it all depends on how much money you're willing to spend, and what functionality you need.


Regardless of whether you go USB or not, I would suggest that you have a seperate computer for machine control, with just the essential software installed to minimise any issues you may have due to random bits of software causing problems.