There is a room after crossing the bridge over the creek that can only be accessed by stepping in some platforms. Inside this room is one of Homer's Duff bottlecap collectables. Behind it a skeletal hand tries to grab a fedora hat. This is a reference to the Indiana Jones series.
In the Planetarium, if you listen to the voice of the man behind the speakers, he'll make a reference to Flava Fav and his clock, Armageddon (the movie) and that he killed the guy who made him read the stuff about the planets.
While facing Kearney he'll say "you guys aren't exactly the Hardy boys" making a reference to the former WWE tag team, The Hardy Boys. Also at the ending cutscene Homer makes a reference to Rowdy Roddy Piper and also The Iron Sheik, both former WWE Superstars.
At the very beginning of the level, is a platform that makes Bart appear to standing on a woman's chest is most likely a reference to Lara Croft from Tomb Raider.