Flaky in Happy Tree Friends is scared a lot of the time, and damn well should be. She always knows that danger will find her in the sadistic world of this show.
Most of the protagonists in the Whateley Universe grew up reading Marvel Comics and DC Comics, and watching lots of anime, so they're pretty well suited to be growing up as mutants in a superhero universe. Deadpan Snarker Phase is probably the most genre savvy of the group. although they all get into the act sooner or later, even the Cloudcuckoolander Jade.
Deconstructed in Sonny Gets Mad Scienced. For all his knowledge about his situation, Sonny's Genre Savvy doesn't actually help him escape. He just happens to be the lucky person on whom the Mad Scientist's experiment worked. Reconstructed when he knows exactly what to do with the henchmen and the scientist when he gets free.
In Survival of the Fittest, v4 character Bounce had been a massive fan of the series prior to her own involvement in it and as such references things like The Power of Friendship never working in SOTF and the fact that, as an unfit, unpopular nerd, there's no point in her making plans because people like her never stand a chance.
In We Are Our Avatars, Awe Striker and Ozbourne, due to being humans from worlds very much like ours, often have familiarity with the fictional universes that many of the other characters come from. This is fairly common amongst most Author Avatars, but a lot of other characters happen to be as well.
This is the source of most of the jokes in the X-Men Flash cartoon "Dark Phoenix Rising". Cyclops references Jean's habit of constantly returning from the dead, the need to put Wolverine on every X-Men team possible and the fact that another group of villains will likely attack while they're being distracted with Dark Phoenix. In "Death Becomes Them", Kitty Pryde asks if the team is counting alternate timelines when they discuss which of them have died and come back to life.
In "84 Egg Sandwich", the employee manning the drive-thru station figures out that the people (Harvey and the gang) are ordering something for an Epic Meal Time project because of how much they're buying.
Cin Wicked tries to avoid the other reviewers in Project Million, stating that he "doesn't want to get involved in crazy shenanigans". He was right to do so.