Ok, well the absolute best ones are:
Abed helping a student give birth in the background of the episode The Psychology of Letting Go. Look at the background action in pretty much the whole episode. It’s amazing. If you count back 9 months, the baby was conceived during the episode The Politics of Human Sexuality, when Abed announces at the STD fair that students should not use condoms if they have sex.
The Beetlejuice running gag – recall from the film that he appears if his name is said three times. In three separate episodes, a character randomly references Beetlejuice, and on the third mention, he appears walking by in the background.
The montage of Jeff and Annie (and later Pierce and Abed) set to “Gravity” in Paradigms of Human Memory was inspired by this real Jeff/Annie fanvid.
And then, there are the allusions to Britta’s disturbing childhood incident with a man in a dinosaur suit.
There are LOTS more, but I’ve listed some of the cooler ones here:
Season 1
Intro to Film – Check out the moves the martial arts students are doing when Jeff says “I don’t want to be your father”.
Physical Education – Look at the people in the background while Werewolves of London plays during the pool match (the song is from this famous pool scene in The Color of Money)
Season 2
Cooperative Calligraphy – Annie’s Boobs steals Annie’s pen on camera at the beginning of the episode.
Critical Film Studies – Abed really did have a cameo on Cougar Town around the time of this episode, as he recounts during his dinner with Jeff.
Season 3
Remedial Chaos Theory – Troy and Abed’s fridge is dressed up like a vending machine… take a closer look, near the bottom (a reference to when Troy and Abed got stuck in a vending machine in a Season 1 episode).
Lupine Urology – did you catch the Law and Order reference in the episode title?
Season 5
Analysis of Cork-Based Networking – Possible Troy sighting