On a personal level, Stewart vs. Colbert, Jon wins. He's simply funnier, and Colbert can only do so much with his persona.
On the satire level, that is reporting things which need to be reported but the media isn't doing it's job, TDS does it more often and it's funnier. Some of Stewart's takedowns (of the idiotic talking-head media, of Michael Brown, on the WMD story, etc) have been historic.
Finally, The Daily Show has correspondents, and variety is always good.
Now on the other side:
Colbert has The Word, which is the funniest segment of either show since Colbert stopped doing This Week In God.
Colbert is a better interviewer by far.
Samantha Bee and the Poll Smoking guy are not very good. The guy they brought on to replace Colbert as the senior expert guy (John Hodgeman?) is good but simply not as funny as Colbert was in that role. Colbert was the funniest correspondent on the show, so that has to give his new program points.
The Daily Show correspondent segments are sometimes simply not funny, especially when they look at weird and crazy things which are not really news items.
By contrast, Better Know a District is consistently hilarious.
In the end... though I like Stewart far better than Colbert... I gotta give the win to the Colbert Report. If you gave me two random clips from TDS and TCR, I would watch Colbert. If you gave me two random clips of Stewart alone and Colbert alone, I would watch Stewart every time.