My absolute favorite type of joke is the one that 90 % of the room doesn't get, and the other 10 % of the room finds sidesplittingly hilarious. MST3K did this better than practically anyone else before or since. ("Community" is the only current show that does this with some consistency.) I actually have about 3/4 of the episodes (maybe more) on VHS in my basement, and I was part of the early "keep circulating the tapes" campaign in that many of my tapes I got from other viewers) I have flirted with pulling them out to watch for a while, but waiting for my daughter to get a bit older.
I always preferred the episodes in which the movies were entertaining in their badness, as some movies were just terribly dull.
I have a special warm memories for "Santa Claus", the Mexican concoction where Santa battles the Devil (well, Pitch) for the souls of children that's even more whacked out then it sounds. (This is not to be confused with "Santa Claus Conquers the Martians", which is a different form of bad.)
I think of "The Killer Shrews" as a favorite, for the fact that the filmakers chose to use dogs with carpets draped over them to represent those deadly creatures...and not even mean dogs, dogs that mostly looked like they wanted to play fetch.
Someone mentioned "Egahh!" (Eegah?) earlier, a quite terrible movie that I quote all the time with wierdly out of left field overdub "Watch out for snakes!" A term I use all the time. (I just googled "Watch out for Snakes" and was pleased to see the first 5 responses all had to do with MST3K.
God, you guys make me want to break into that bin in the basement!