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 at least 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.
Tearjerker: Then Servo asks Joel why doesn't he just not die, as if death is a decision people make.
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 linear superposition". He thoroughly demonstrates it for Joel and Crow.
Servo:(as Sam Bass) Hey, lady, you forgot to tell me where the — Oh my God! AAAAAGGHHH!!!
They Just Didn't Care: Despite Tom's insistence that some advanced physics is going on, Crow repeatedly remarks that the town is just a bunch of false fronts, and that the filmmakers actually seem to be incorporating that fact into the movie.