I'm of the opinion that the Best Show started great and just got better as it rolled along. However, in retrospect, for a newcomer some of the shows of the first couple of years can be slower-paced and possessed of an unsure identity, as Tom used to play a lot more music (some of the really early 2000-2001 shows, when TBSOWFMU was only two hours long, can be more music than talking). On the other hand, you really don't want to miss the "origin stories" of some of the Wurster characters that are located here. Philly Boy Roy, in his first few appearances on TBSOWFU, had a much different accent and cadence to his voice, for instance. Also, the incomprehension of many of the unsuspecting listener/callers is fascinating to behold - it's easy to get used to the parameters of the show as it exists right now and not realize that the first years, when the audience was mostly local and used to WFMU as *music* station, Tom was truly fighting an uphill battle in getting a show this radically different from all previous radio call-in shows heard and understood. In that light, the first couple years approach a prankish dada theater aspect at times. The Best Show certainly has a much more "underground"/samizdat kind of feel during the first couple of years, particularly whenever Jon Benjamin appeared (solo, or with Jon Glaser); what Tom and co. were doing here was pretty daring, when you consider the context.
As the show progresses, regular callers come, stay for a while, go, reappear; if you're not an Officer Tom fan, skip over the 2002-2006 period. (But why wouldn't you be? He and Tom had a great, easy rapport). Likewise, if you're not a Petey fan (Now THAT I can understand), you may want to skip around some more. This era is where, I think, Tom really comes into his own as a talker/conversationalist/monologuist/raconteur. One of my favorites from this era is the 100 Best Movie Quotes show (June 28, 2005: Tom Starts To Assemble A List Of The Top 100 Movie Quotes To Counter The Dopey AFI Quotes List. Everybody Calls In! Philly Boy Roy Drops In. And NBA Star Mehmet Okur Calls In To Discuss His Love Of Surfing.), because of the rapid-fire patter between Tom and the callers. One other thing that this show (and many others of the period) does is solidify a certain aesthetic around The Best Show and in particular around Tom's own sensibilities; when Tom dispatches many of the callers' quotes as too pedestrian or a bad fit for the list, what emerges is a full picture of Tom's own tastes and preferences (The humor of "Caddyshack," for instance), which heretofore inform the Shows to a much higher degree. The Newbridge mythology gets superthick during this era too. (It's also clear that more listeners are finally catching on that not everything on TBSOWFMU is what it appears to be.)
With the move to a podcasted Best Show in 2006, the show gains incredible popularity and hits a plateau of incomparable excellence for the next few years. "Celebrities" begin to appear on the show more and more, 2008 Mayubenatorial Race routines get truly crazed, Tom and Jon hone their dialogues to fine a fine diamond-y luster, etc. Pretty much every show from 2006-2010 is a "W," in my book. Particularly good shows during this period include 4-22-08, 7-21-09, 6-03-08, 11-24-09, 6-15-10. But essentially it's all of a piece, a piece of such high quality that every show is worth a listen.
A little past halfway through 2010, Tom takes a break, obviously fatigued by the effort he's put into creating something this monumental over the last ten years. Surrounding that break, however, are several shows that are exceedingly dark and personal affairs, full of soul-searching, sadness, anger, etc. Frankly, they're painful to listen to. Since then though, TBSOWFMU has come back hard, each show professional and polished. I pine for the return of some of the early Wurster characters like Zachary Brimstead or the rockers in POUT, but whenever Jon appears, it's a triumph. Also, Mike has emerged as a major player in the Best Show saga, becoming Tom's muse and foil. Gary the Squirrel's ascendance is also something to celebrate. The Four Loko episodes are fantastic, as are the 5-19-12 and 8-14-12 shows. But again, the same old story is that it's all of a single piece - the Best Show, as a totality, rises from the cultural landscape like an earthwork. (The iceberg goes *incredibly* deep.) Individual shows may be gems, but I agree with others that the whole is greater than the sum of its parts - go back and listen to the show from the beginning to catch the continuity of everything: the unfinished jokes that resolve themselves in later episodes, the self-references, and the evolution of a community.