There were so many. At the moment I'm waiting on a new copy of the game to arrive (my sound was faulty so I decided to get a new one) but I was thinking that I probably missed a lot of the jokes in the game since some where fairly specific.Like Eel Infested Waters was clearly a nod to The Princess Bride and at the moment the only one I can clearly remember.
Are there any others I might have missed. I don't mean things like traditions in the series but rather specific little cultural references within the game.