Is that really the audience laughing at Colbert, or a laugh track? The reason I ask is that there is a guy in the audience with a really distinctive laugh that I hear every single night that I watch The Report.
It occurs at precisely 3:15 of this episode: http://www.hulu.com/watch/100848/the-colbert-report-wed-oct-7-2009
And I’ll keep an ear out in future episodes so I feel less like a crazy person 
Here he is again at 12:19 http://www.hulu.com/watch/100848/the-colbert-report-wed-oct-7-2009
It’s a real audience as far as I know. The laugh could belong to someone associated with the show so is regularly there.
If the laugh is that distinctive on the show, it’s probably someone close to a mic, like a cameraman or floor producer.
Another vote for the laugh belonging to a crew member that’s probably close to a mic. The same thing happens on The Soup where a few distinctive laughs can regularly be heard.
I’ve been in the Colbert audience twice. They don’t use a laugh track.
When I did the NBC tour, they showed us microphones hanging from the celing above the audience that not only amplified the crowd, but ran it through two or three times to make it sound like more people.
Well this crew member apparently loves his job and thinks Colbert is far funnier than I do 