I'm making this thread based around my theory there are a fair number of MST3K fans around here. I figure, the worst that can happen if I'm wrong is this thread will die a slow death until it disappears somewhere on Page 35.
I'm a Joel groupie, and my favorite ep of all time is "I Accuse My Parents". It's not Sci-Fi or Mystery, but to me it's the tightest and funniest episode ever. The set pieces are just as funny as the wisecracking in that one, and it's the one I quote the most (hamburger sammich with french fried potatoes garnish, anyone?). Tom Servo's opening song on that one is the best one ever.
I also have a soft-spot for "Red Zone Cuba" and the endless Coleman Francis jokes.