The Dog Bites Back: When Dr. Forrester attempts to scan TV's Frank's brain (and accidentally blows up a lightbulb in the lamp), Frank gets really cheesed off when he realizes it.
TV's Frank: You were scanning me, weren't you? You were trying to make my head explode, you freaked-out maniac! [smashes Forrester's head with a large lolipop.]
The Fun in Funeral: During one of the host segments, Joel and the bots get to experience death... or what it feels like to be in a casket. After a moment contemplating what death would be like, they start describing how they want their funerals to be like - Crow's and Tom's are really fun.
Kill 'em All: Thanks to the fact that most of the extras playing townspeople just up and disappear for the last third of the movie, Crow and Tom run with the idea that the entire town is dead.
Offscreen Teleportation: Tom Servo explains that the examples of this trope in the film are examples of applied "quantum superposition". He thoroughly demonstrates it for Joel and Crow.
The movie is flat-out incorporating the fact that the town is just a bunch of false fronts in a few gunfights by the end: They Just Didn't Care.