9. Digital Estate Planning (Season 3, Episode 20)

Ah yes, the 8-Bit episode. It was so unexpected and brilliant that it simply had to make the top ten. This is everything Abeds Uncontrollable Christmas should have been. So popular it spawned an actual fan-created mockup (available from Reddit), we see Pierce discover a brother, Abed finding love and Troy and Pierce losing at strip poker. Its just so original and out-there, its definitely one of the shows most creative episodes, engaging me in a medium Ive never really warmed to.
8. Pillows and Blankets (Season 3, Episode 14)

In a similar vein to Basic Lupine Urology, the epic tale of Troy and Abeds divide between The Legit Republic of Blanketsburg and The United Forts of Pillowtown (its hard to choose a side- I choose Pillows, but Id much rather be led by Troy than Abed) parodies the type of civil war documentaries you see on the History channel, the Discover channel or National Geographic. This has too many priceless moments to mention. And, like all the best episodes, there is something of a dark edge to it all with Troy and Abeds hurtful messages to each other. We see a close and child-like friendship turn nasty and be truly tested.