South Park and Family Guy still have a good following, and to their credit they still have some good episodes. The opener to season eight of Family Guy is one of the best episodes of anything I've seen - but that could be because they deviated from their usual scriptwriting and had 21 minutes of Stewie and Brian locked in a room. South Park was good at the start but it got too political.
I know "Reincarnation," and I don't mind that one. The anime section is probably my favourite in that episode. I like the ones that make me think and have maths and science all through it. "The Why of Fry" from season four is a great example of this and stands as one of my absolute favourites. "The Farnsworth Parabox," "The Duh-Vinci Code," "Three Hundred Big Boys," "Roswell That Ends Well," and "Future Stock," among many others, are awesome episodes because they require some thinking and have great writing that ties it up well at the end.