I've never heard of MST3K.
I was thinking of starting an animated thread, but that just boils down to The Simpsons, South Park and Family Guy (although Transformers would get my vote). If anyone thinks this is worth while start one up, that can be a whole other discussion that would fill a void in a boring off-season.
You, my friend, need to start watching Adult Swim. Over the last several years they have put out some of the most unique, clever, and funny programming out there, animated or not. I'd recommend Venture Bros., Aqua Teen Hunger Force, Sealab 2021, Squidbillies, and Harvey Birdman for your viewing pleasure.
Other shows that may collect votes would be The Critic, Duckman, 3 South, Dr. Katz, King of the Hill, and Spongebob Squarepants. And am I the only one that loved Muppet Babies growing up?