While Manos is a go to episode ( mostly because it’s the only way to make that flick remotely watchable ), I’d have to say that the funniest episodes of MST3k are Space Mutiny and Cave Dwellers.
Space Mutiny is on Netflix right now, go watch it if you haven’t seen it, and get ready to bow before Reb Brown’s manly war cry while driving a tiny zamboni. The Cave Dwellers episode is a bit harder to find, but it’s far and away the one episode that consistantly gets a great reaction, every time.
“ How much Keefe is in this movie? MILES O’KEEFE!!! “ Classic.
Pumaman is also a worthy mention, if for no other reason than to wonder what the fuck bet Donald Pleasence lost to be in it
Edit: Found this for you guys, go make some popcorn and enjoy.
https://youtu.be/ZKO6M8heGU0