Number of times reference is made to the following:

1.Batman (Adam West TV show)
2.2001
3.Hooterville Trilogy
4.Lord of the Rings
5.Monty Python/Fawlty Towers
6.The Bible
7.It's a Wonderful Life
8.Star Trek
9.Dirty Harry
10.Other movies shown on MST3K

If you can think of any others, add them on.

Oh, I forgot:

11.The Princess Bride

As you wish, Gordon.

And let us not forget Circle Pines (creator Mary Jo Pehl's hometown), the standard small-town riff - referenced for example at the very beginning of 'Eegah!'.
Also - as far as i can tell from about 15 Rhino tapes - whenever there's a scene of a woman driving, Tom Servo inevitably sings the first few bars of the Mary Tyler Moore Show theme: "How will you make it on your ownnnnnn...."

And then there's Crow's ongoing fascination with the tagline from the old Palmolive (dishwashing liquid) commercials: "....you're soaking in it!"

Whoops, I just posted something similar to this in "Obscure References." I'll re-post it here.

A man forcing himself on a woman is always accompanied by a Senator Packwood joke. "Oh-ho, it's Senator Packwood!"

A man on his knees or with black stuff on him will usually be accompanied by "Mammy!", in a reference to Al Jolson.

Post-Manos, there is occasionally a reference to that throughout the series. Other hack filmmakers sometimes get referenced, such as Roger Corman.

'Trumpy, you can do magic things!!' (a la 'Pod People') shows up in a lot of other eps, too.

"Oh, I have tubes in my ears."

Wizard of Oz and 2001 are probably the most referenced, at least as I've seen.