My vote is for the 07 mostly because its the dual spark model. The dual spark motor is much smoother, a bit more power, and better fuel mileage, but best of all, doesn't suffer from the surging some of the early models were known for.
Plus, I tend to really stay away from bikes that have sat for awhile. There almost always turns out to be other issues you didn't anticipate.
That's not a bad price for the 07 either and super low mileage. My wife has an 06 F650GS with about 30k on it and I really enjoy riding it myself. Its a great bike.