As of earlier this
morning (8:00 AM EST), there is a page for both The Colbert Report [iTunes link] and the
Daily Show [iTunes
Link] in the iTunes Music Store, though they still do not contain any available episodes.
The sale of these shows is being handled a bit differently. You can buy a "multi-pass" for both The Colbert Report and The Daily Show for $9.99US. This gets you the current episode, and sets up iTunes to automatically download future episodes as they become available (up to 16 episodes). Think of it as a paid podcast.