I started watching back at the start of the 2nd season when Dr. Earhardt left and Frank joined. It's hard to pin down a favorite episode. Obviously Manos comes to mind because of how awful the movie itself is, but I think there are some others that were funnier overall. Some of the weirdest were Japanese, like Mighty Jack, Fugitive Alien, and Time of the Apes. They're all good though.
Have you heard about The Film Crew? It's Kevin Murphy, Bill Corbett, and Mike Nelson (Servo, Crow, Mike) doing commentaries for bad movies again, but direct to DVD. They are playing themselves though, not the MST characters.
There's more info here: http://www.filmcrewonline.com/
Also, Mike Nelson does RiffTrax, which are MP3 commentaries (sometimes with other people from MST or elsewhere) that you download and watch along with your own DVD. Most of these are for big budget movies such as 300, Star Wars Episode 2, Fantastic 4, etc.