One Regular Show fanfic features Mordecai and Rigby jumping out of the show using a "Cartoon Leaper 3000". They even proclaim that "This show is getting boring anyway!"
Han: Excuse me as I break character here: To the author: About this dialogue, are you on some form of illegal substance? Wedge: And could we please have some?
In context, however, Han's only breaking the fourth wall in a play they're rehearsing.
Pinkie Pie breaking the fourth wall to acknowledge or even directly address the readers and/or the author is something of a Running Gag in FiM fanfiction in general. Sometimes other characters get in on the act, more often it's waved off as her just being Pinkie.
In The Last Airbender parody Bring Me All Your Elderly, the Animated!Characters not only are aware that they are animated (and discuss it very casually), they also leave the Animated!Universe to enter the Movie!Universe, generally blame all unexplained events either on the fanfic author or M. Night Shyamalan, read their own fanfic and comments straight off the internet, and basically suffer severe existential crises as a result. The fourth wall itself actually makes a brief appearance at one point in the story, along with a sign that says "fragile."
Mai: But for future reference, guys - try to be careful about breaking the fourth wall around Zuko, okay? He doesn't know, and it tends to freak him out a little.
Zuko: Fourth wall? What wall? Someone broke a wall?
Mai: Nothing, Zuko. Just don't worry about it.
In the Naruto "Quiet" fanfiction by MaliceArchangela, partway through the first story Quiet on the Golf Course, Itachi Uchiha starts routinely breaking the fourth wall, speaking with the author to the point that the breaking happens every chapter, and allows reviewers to communicate with Uchiha.
One Star Ocean fanfic titled Aquios High has one memorable scene where Cliff, under the influence of some sort of drug (I can't remember, think it might have been alcohol), explains to everyone about the authoress responsible for everything. Since the author decided to turn the fic into an actual book, it might not be online anymore.