I think the season two version is the best.
A bit longer than the season one intro, added singing in the background, and DeForest Kelley is added to the credits. Season three is virtually the same, just with blue text. That season sucked though, so I can't pick it

TAS has nice intro music, a cool variation on the original Alexander Courage theme song, but the animation with the ship flyby sucks. Also, I prefer the TOS music just that little bit more.
What's your favourite version?