In an issue of Marvel Adventures, at the end of a Let's You and Him Fight Spidey says, "It was a textbook superhero misunderstanding battle. Happens all the time! Luckily, this is the part where we make up for it by working together to stop her."
This actually happens a lot. Nocturne in Exiles refers to that as an "unwritten rule of superhero team ups" and Robbie from Nova is disappointed that Darkhawk and his brother didn't do this.
Zombies Calling by Faith Erin Hicks is built around the main character being savvy to the "rules" of zombie movies.
In Alan Moore and Dave Gibbons' Watchmen,Adrian Veidt, aka Ozymandias, declares that he is not a villain from a Republic Films serial and therefore had already completed his plan 35 minutes before beginning his Breaking Speech.
Also, referring to his first meeting with the Comedian (where they fought before realizing they were on the same team), Adrian comments on how common a misunderstanding this is in their chosen profession. This is a reference particularly to Marvel heroes, who will ALWAYS battle EACH OTHER upon first meeting.
In The Sandman, Morpheus is possibly one of the most genre savvy entities in the whole universe. As the Prince of Stories, he knows that life literally imitates art (and vice versa) and is more than capable of controlling it. While teaming up with John Constantine to enter a house haunted by renegade dreams, Constantine shows some genre savviness himself, recalling what happens to people in horror movies when they split up. He asks Morpheus for reassurance that they'll stick together.
In Uncanny X-Men # 143, Kitty Pryde declares: "If this was a movie, the monster would be waiting right outside the door, ready to bite my head off the moment I show myself."
Kitty (sitting at the computers): And then nothing. Look, the whole board rolled over and died.
Colossus: It could be nothing, Katya.
Kitty: It doesn't feel like nothing, Petey. I can't raise Scott's team either. I even pinged Cable in Providence, and guess what? More deafening silence.
Colossus: Do you want me to take Blackbird Two and rendezvous with Scott and the others?
In Return To Wonderland, Calie is nearly raped by The Hatter, but she gets the upper hand and knocks him out. She declares that she will not repeat the mistake that girls usually make in horror movies (knocking out the bad guy, then leaving the room), and continues the beatdown on Hatter until pretty much all of his bones are broken. It doesn't stop him from coming back. The inhabitants of Wonderland are eternal and eventually reappear every time they die, but Calie didn't know that.
In Ultimate Spider-Man, Bolivar Trask demonstrates this when he asks if the stasis field in the lab he's in can contain Venom. When he's told that it can, he says that he's seen King Kong, and so will be leaving.
In the 1991 Marvel Year In Review, Greg Salinger (the second Foolkiller) is interviewed about the activities of his successor, Kurt Gerhardt. Salinger opens by stating that Gerhardt's father had been killed by muggers. When the interviewer inquires as to whether this was the motive for Gerhardt's vigilante actions, Salinger responds by saying "Don't be so cliché".
Don Rosa: When the Ducks are pursued by a hungry Spinosaurus in Escape From Forbidden Valley, Uncle Scrooge suggests taking a shortcut over a cliff across an old wooden log. His nephews immediately dismiss the idea and snark that the last movie their uncle has watched was probably at a 1904 science expo.
In Violine, Muller blindfolds Violine to prevent her from reading his mind, and other characters wear sunglasses to prevent this as well.