Okay, this is the list of all the things I can think of that are parodied/referenced all the time starting with what's been mentioned here:
Star Wars
Indiana Jones (boulder thing)
Jaws (mostly just the signature score)
Matrix slow-motion stuff
The Wizard of Oz, usually involving a black and white beginning scene
A Christmas Carol
Citizen Kane (Rosebud is used a lot)
Willy Wonka
The Godfather
Harry Potter
Lord of the Rings (my precious)
Superhero comics/movies in general
The Good, the Bad, and the Ugly (most "western episodes" will have a reference to this somewhere)
Psycho (the music)
It's a Wonderful Life
Saving Private Ryan (a lot of action spoofs will parody the shaky-cam)
The Sixth Sense (usually with someone yelling a spoiler... I've never even seen this movie and I know the ending because of all the references to it)
Scarface ("say hello to my little friend" is everywhere)
Most anything by William Shakespeare, but mostly Romeo & Juilet, Hamlet, and Macbeth
Popular horror icons: Frankenstein, Dracula, etc
Planet of the Apes (especially the ending)
James Bond
Rocky ("you talkin' to me?")
Star Trek
Pokemon (at least it used to be parodied all the time)
There's probably a million others. It seems like references have become a substitute for jokes in recent years.