And in the same vein, Sailor Moon Abridged regularly points out its plot holes, and one of the scene transitions is Serena saying "plot hole!"
In the Broken Bow series, book 3, we get this lovely exchange when Ari Mc Murphy, who is incidentally a child of the Goddess of Chaos, keeps saying things like "At least it can't get any worse!" Things, of course, immediately get worse directly afterwards.
Played straight, and then lampshaded in this chapter of a Warhammer 40000 fanfic, which has the main character bash an Eldar Farseer and Space Marine Terminator with a fire extinguisher in much the same way as he did the previous chapter, gives a snark about the possibility of it becoming a running gag, then goes on to extinguish the smoldering lampshade behind him.
Chapter 8 of Takamachi Nanoha of 2814 by Shadow Crystal Mage makes fun of this trope, repeatedly having characters ask where other characters want lampshades hung, or variations thereof. It also plays this trope straight, sometimes in the same paragraph as the gags.
A Very Potter Sequel has a (seemingly) improvisational instance of this. There is a scene where Ron attempts to pull a poster of Taylor Lautner off the wall in Umbridge's office, but it appears the actor has too much trouble trying to tear it down and ends up returning to the group, saying "it's stuck on with magic!" When they appear in the next room — which is the same area on the stage they just "left" — they comment on the fact that "there's a Taylor Lautner poster in here, too!"
In thisGlee fanfic, Rachel pretends to be a boy so that she can enroll at Dalton, and ends up being Kurt's roommate. Upon finding out that she'll be rooming with the only person in the place who is in on the secret, she says: "Oh. Well, that's ridiculously convenient."
Obsessive Lily Disorder The story is set in the seventies and Sirius is singing a lot of more modern songs. James points this out:
"Sirius, for Christ's sake," James sighed, "Will you ever stop singing random songs that probably haven't been written yet and are completely out of this time period?"
In Fantasy Sports League: "It's unprecedented! In the history of literature and sports I don't think there's ever been a case where a group of ne'er-do-wells were able to band together and in the most unlikely of conditions, take on an all-powerful foe! This is amazing!"
Those Lacking Spines is, without a doubt, the single most lampshade-riddled fanfiction ever. It takes the time to bring up anything and everything ever done by a fanfiction writer who wrote about Kingdom Hearts and Organization XIII, and proceeds to mock it and deconstruct it in every single way possible.
When Terra expresses surprise that Jump City has a diamond mine, Cyborg states that the city has a lot of stuff, and that he sometimes still gets surprised. This most likely is in reference to the fact that the city's layout on the show often seemed to change depending on the needs of each episode.
Jinx at one point wonders why buildings always end up on fire when they're attacked by villains.