Annie's story about her high school boyfriend, is based on something similar that happened to Alison Brie in real life (though it was her friend she slept with, not a high school boyfriend).
During the hand wrestling between Troy and Abed, Abed flexes his fingers before winning. This is a reference to the Stallone movie Over the Top.
Annie is asked if she's ever seen a penis on TV, like Harvey Keitels. Harvey Keitel was fully nude in Bad Lieutenant which played frequently on late night cable.