My favorite trick that Farscape used twice is to take the arch-villain and make him part of the "crew". I used it in my current D&D campaign.
It is soooo cool when you build up an villian over several sessions and then make his goals and the PCs' goals the same. Having the PCs work with someone they don't trust, expecting the whole time to get hosed over at any moment is a blast. It's that "deal with the devil" kind of feel that you get when John and Scorpy have to work together.