I looked through again and didn't see this one so...
Captain Reynolds (shows up in a few spots in Cool Ranch) is supposed to be Mal Reynolds (Nathan Fillion) from Firefly. He even gives a quest to help a doctor (who has a strange crate of cargo) get to safety.
It looked like there was some deliberation over whether or not the three horse singers were supposed to be the Three Amigos or just coincidence. Their name, collectively, is Dos Amigos y Uno (2 friends and 1...or 3 amigos).
The great turtle in Mooshu (the one with the city on its back) bears a striking resemblence to the large, wise turtle from the Neverending Story movie.
Throughout the Temple of Serenity there are a bunch of Masters with names like "Master Wa" Master Hao" Master Wen" ... allusions to Who, What, When, Where, Why and How.
The Abe Pagoda is a tribute to Abe Vigoda, an old actor "Fish" from Barney Miller in the 80s.
This game is just chock full of references. It really feels like pretty much everything has a reference to something. There truly are too many to list. We would literally be here for weeks just listing every little thing that this game "hides" within its world.