I just ordered — and may someday have the time to actually read — a new book by Chris Smith called The Daily Show (The Book): An Oral History. It's interviews with darn near everyone who worked on the Jon Stewart years of The Daily Show so how can that not be interesting? You can read about some of its more interesting revelations here and you can order a copy here.
Sorry to hear it only mentions the Craig Kilborn years in a negative context. Kilborn always seemed a bit infatuated with himself but the show was very entertaining when he was its anchor. Some people now seem to recall that Stewart took over a lousy show and made it great. I think he took over a good show and made it better.