When Jeff reads out Abed's file, Abed's patient number is 1373, which is Community creator Dan Harmon's birthday - 01/03/1973.
The Dean comes in dressed half man/half woman. Before WWII this was a common sideshow performance called the heshe, half and half, or hermaphrodite. The performers would go so far as to strenuously exercise only the male side and protect the female side from tanning.
When Abed is impersonating Jeff, the vending machines in the background are selling buttered noodles. At the end of the episode, Abed makes buttered noodles for lunch.
In Abed's medical file, it shows that his Attending Physician is Dr S. Gagossian. This is a reference to Shoghig Gagossian, Set Dressing and Props Production assistant on the show.
When Abed is freaking out at the end, Troy says "cut, Garrett." Garrett Donovan is an Executive Producer of "Community." Also, the character Garrett in the show is often seen as a cameraman for their films.