I truly appreciate how these two shows take the right wing to task. They constantly point out that "the emperor has no clothes" and that is much needed. Though often funny, they can be quite vulgar.
Those things being stated, they are both liberal in many respects--Colbert more so than Stewart. Stewart is a secularist, but comes off as more respectful of religious expression in general (when compared to Colbert). Colbert, who is Catholic (at least he claims to be), tends to vile in his treatment of religion, especially Christianity.
I often torn when I watch these shows--on one hand I thoroughly enjoy how they turn the spotlight onto hypocrisy, especially conservative hypocrisy, but on the other I find the shows almost unwatchable when they use Jesus as a punchline. All in all, Stewart's show is much more well rounded in its treatment of the political spectrum and religion, while Colbert tends to be more extreme.
I definitely prefer Stewart because of his wit, presentation, and knowledge. However, I find Colbert funnier because of his bald-face ability to imitate. It's absolutely hilarious that so many in the right-wing news like Fox despise him. He is them. The sweet taste of irony.
But Stewart is by far the better commentator of the two plus his ability to hold his own in his debate.