Via Jaime J. Weinerman. This article delves into the hidden complexities behind releasing older TV shows that contained licensable music. It's really a shame that licensing fees have gotten so out of hand that it's actually not profitable for a studio to release the show as it originally aired.
I remember the episode of Quantum Leap that they mention in the article and I can see why fans would be angered about that particular song replacement - music is often a powerful memory cue and that was an emotionally charged scene. Changing a memorable theme song to a show, like Married with Children is absolutely inconceivable to a nostalgist whose whole raison d'etre is to relive the experience (not live a new one).
I think the WB television show Smallville uses music found only in the Warners music library. I think this serves two purposes: the obvious one being that it's free advertising for the music (much like the early WB Merrie Melodies cartoons were), the non-obvious purpose is that, as long as WB continues to release the season DVD sets of Smallville at a rapid pace (instead of lagging a few years behind where music rights could possibly change hands), there will never be any licensing issues with the music used in that show (though I'm sure that money still changes hands between businesses within Warners).