These aren't my "Top 10" as much as "10 of My Favorite TTRHs"... I liked the music on all these - but I can say that for nearly any of the 100 TTRHs. These are the ones that stand out in my mind for more than the music.
1. Weather - Because it was the first and set the standard for the rest.
2. Baseball - Mr. D. doing an a capella Take Me out to the Ball Game
3. Flowers - The leader in def poetry readings and the bonus of Tiny Tim.
4. Friends & Neighbors - The "What happened to country music?" rant.
5 (tie). Halloween/Christmas and New Year's - "The Raven" and "A Visit from Saint Nick." Plus both handled a holiday theme without crossing over into Dr. Demento territory, or even "Christmas Party with Eddie G." territory.
6. Days of the Week - The "Commercial Affiliations" rant.
7, 8, 9. California, Classic Rock, and Cadillac - The Three Big C's from `07. I thought these three consecutive shows that ran in the early part of Season 2 were arguably the apex of TTRH.
10. Goodbye - Not only because it was the last, but you could tell the TTRH team wanted to go out with guns blazing... and they did.
Thinking it over, I'm biased towards Season 1, probably because I've re-listened to those shows more than the other two seasons. But I've found I like Season 2 more than I did when it first aired. I just re-listened to "Walking" for instance, and found I liked it a lot better than I remembered from the first time around.
I still feel that Seasons 2 and 3 weren't as strong overall as Season 1, although there are individual shows from each season as strong as anything that aired during Season 1. And I go back now and listen to some of the early shows and I'm amazed at how much Mr. D. grew into his deejay role over the three seasons. The first few shows you can almost see him and Eddie G. groping around for something for him to say... lots of repetition of lyrics when they had nothing else, with Bob doing his patented inflections. By the end he sounded like he had been broadcasting from the Abernathy since Methuselah was a pup. Go listen to "Weather" and then "Goodbye" to hear what I mean.
Anyway, as I said, "10 of My Favorites." I could have easily picked ten others. And probably 10 more after that. But I'm a fanboy.