Stargate: SG-1 had an amusing self-parody episode about the making of a TV series called Wormhole X-treme. There were several references to fans’ nitpicks, such as this:
Yolanda Reese: “Uh, I’m having trouble with scene 27. It says I’m out of phase, so I can pass my hand through solid matter, or walk through walls.”
Director: “Yeah, yeah, cos you’re out of phase.”
Martin Lloyd: “Um, exactly.”
Yolanda Reese: “So, how come I don’t fall through the floor?”
Long pause, with Director and Martin staring at each other
Martin Lloyd: “We’ll have to get back to you on that.”
I don’t know if this counts, but in one episode of Monk, they threw in a sly reference to the complaints that fans had after Jeff Beal’s Emmy-winning instrumental theme song was replaced in the second season with a new song by Randy Newman (which also won an Emmy). In a case involving an actor in a CSI-style show, one woman is seen asking people to sign a protest for his show to go back to the original theme song. At the end of the episode, she thanks Monk for getting her idol off the hook, saying he’d be a great TV star, too. Monk disagrees. She says to him, “Promise me one thing…if you ever get your own TV show, don’t change the theme song.” The episode ends with Monk’s original theme.
This was actually in a later episode, during a parody of Billy Joel’s song We Didn’t Start the Fire. Although there was a jab at the idea that The Simpsons’s quality was declining in this episode, too- Troy McClure promises that there will be more fun ahead next year with “America’s favorite family…and a little green alien named Ozmodiar that only Homer can see” (a reference to The Flintstones’s Great Gazoo, by which point the show’s writers had obviously run out of ideas). There was also one gag regarding the show’s longevity and quality (or lack thereof) that took two seasons to get to the punchline of: the final episode of the show’s 12th season opened with the Simpsons at an airport kiosk for Air Delaware. Homer exclaims, “The Simpsons are going to Delaware!” Lisa shouts, “I want to visit Wilmington!” Bart adds, “I’ve always wanted to visit a screen door factory!” This, in itself, is a funny play on the number of episodes in recent years which involved the Simpsons travelling to another country, most of which did feature Homer shouting “The Simpsons are going to [insert exotic locale here]!,” but to fully get the joke, viewers had to remember the final episode of the 11th season, which was a parody of Behind the Music tracking the ups and downs of the Simpsons’s career. The second-to-last scene* in this episode featured Homer looking on as a producer is viewing a cut of a future episode: Homer exclaims, “The Simpsons are going to Delaware!” Lisa shouts, “I want to visit Wilmington!” Bart adds, “I’ve always wanted to visit a screen door factory.” Homer looks at the producer assuredly and says, “This’ll be the last season.”
[sub]*The last scene in the show is a preview of next week’s Behind the Laughter “episode”: the Huckleberry Hound story. “I was so gay…but I couldn’t tell anybody!”[/sub]
this is according to my sister, who insistst hat it happened, even though I don’t remember it.
Morgan, the lttle sister, apparently disappeared for a few seasons. At some point, someone said, “wait, didn’t we used to have another kid? whatever happened to her?” and she (played by a new actress) came on and said something like, “wow, I’ve been in my room a long time!”
Also, there’s one episode I KNOW happened- Eric (the older brother) gets a part on a sitcom- "Kid Gets Acquainted With the Universe"where they make fun of the show.