Your sig doesn't list the year of your bike, but I think there's only two options:
1. Power Commander III USB (I think it's for 2002 and above -- correct me if I'm wrong). Uses USB for connectivity, and has a slightly better GUI.
2. Power Commander IIIr - standard serial connection, but can also modify timing pulses. That's not really necessary for a stock bike, but if you're doing turbo/engine work, it's a definite must. To do the timing thing with the USB, you have to buy the timing module which practically doubles the cost.
If I'm wrong on any of this, let me know, and I'll edit.