Not stock as in repeated and expected, but something you just know the writers came up with in a brainstorming session years before they actually dusted it off to use in an episode. These two seem fairly obvious candidates. They didn’t seem to be inserted at a particularly appropriate time, versus any other episode:
– Focusing on Mr Burns while playing the Imperial March.
– D’oh! A Deer! A Female Deer!
This isn’t quite what you were asking, but the OP brought it to mind, so here goes.
The Futurama episode “Where No Fan Has Gone Before” ends with the credits over a series of freeze-frames, a la Classic Trek. Last of all is a shot of Kif.
I’ve never read anything to confirm this, but I strongly suspect that it was a deliberate decision to make Kif look like the gray/green alien guy in the last shot of the TOS credit sequence. Because with a show like Futurama, a Trek parody is a matter of not if, but when.