There can be a very good case made for The Venture Bros. being a deconstruction of Jonny Quest and Doc Savage-style stories. Some say spoof, some say deconstruction, some say both. The main character is a former Kid Hero who, due to a childhood spent traveling the world with his Adventurer-Scientist father, has seen and done things no twelve-year-old boy really should have to, and has grown up into a bitter, pill-popping, barely-functional human being. His rugged Action Hero bodyguard is basically the kind of borderline sociopath that would gravitate to a world of clandestine doings where brutal murder is an acceptable way of solving problems. His children are socially awkward nerds, but not in any of the "good" or "endearing" ways; they were basically raised in boxes and have no clue how to interact with reality. And his arch-nemesis is a lame animal-themed Super Villain who, despite moments of competence, is so wrapped up in planning the details of his over-elaborate and petty revenge schemes against an enemy who barely knows who he is that his schemes never actually get off the ground.
Looney Tunes director Chuck Jones often used deconstruction on his cartoons. The best known example is Duck Amuck: First the scenery changes, forcing Daffy to adapt. Then Daffy himself is erased and redrawn. Then the soundtrack fails, then the film frame, and so on until Daffy is psychologically picked clean. Another example is What's Opera, Doc?, which takes the base elements of a typical Bugs Bunny cartoon and reassembles them as a Wagnerian opera. (Conversely, you could also say that it takes the base elements of Wagnerian opera and reassembles them as a Bugs Bunny cartoon.)
Family Guy does a particularly nasty deconstruction of Looney Tunes and its Amusing Injuries, wherein Elmer Fudd is out "hunting wabbits", shoots Bugs Bunny four times in the stomach, snaps his neck amidst cries of pain, and then drags him off leaving behind a trail of blood. In another episode where Peter and friends became The A-Team, the show's "amusing injuries" are discussed as actually life-threatening.
The famous Simpsons episode "Homer's Enemy" is a deconstruction of the general weirdness and insanity of its setting, based around the premise of What if a real-life, normal person had to enter Homer's universe and deal with him? Frank Grimes, a relatively humorless but hard-working man who is still forced to live cheaply despite working almost his entire life, encounters Homer on the job at the nuclear power. You can imagine what happens next - the result is funny, but also disturbing and very dark upon further reflection (one of the darkest Simpsons episodes ever made).
At one point, Homer is about to drink a beaker of sulfuric acid when Grimes stops him. Grimes reacts exactly as we would expect a normal person to react — he's visibly freaked out, and when Homer blows off the danger with laughter, he shouts, " Stop laughing, you imbecile! Do you realize how close you just came to killing yourself?!" A series of such incidents ultimately drives Frank Grimes into insanity and death.
The episode eventually winds up in Crosses the Line Twice territory when, at Frank's funeral, the "mourners" do not cry but rather laugh when Homer dozes off and mumbles some idiotic gibberish. Even the minister.
The episode also highlights the absurdity of one man having such a rich and adventurous life (meeting Gerald Ford, winning a Grammy, going into space...)
Iron Man: Armored Adventures offers an interesting take on the teenage superhero genre in the fact the hero really couldn't care any less about school or fitting in, claiming it's a waste of time and instead stating that his work as a hero is more important. He then proceeds to cheat on his tests and homework in order to pass, since him being a hero gives him the latitude to do so, and high school is meaningless and doesn't matter once you graduate, especially since he's already a)rich, and b)a genius inventor.
"Epilogue" of Justice League Unlimited can be taken as a deconstruction of the superhero genre by having a Amanda Waller deliberately try to engineer another Batman in response to the original Batman growing older. It fits both invoked and deconstructed, because it shows the horrible consequences of making a superhero, as well as the kind of monster you would have to be to do it (killing innocent people to do something that might achieve a goal).
It also deconstructs the classic Batman origin: Waller plans to kill Terry's parents when he's a boy, but when the assassin she hires (Andrea Beaumont, the Phantasm) refuses to go through with it, Waller realizes that whatever her goals, it wasn't worth it, and she's pleased that Terry has become a much more sane and stable superhero because he had a chance for a normal childhood.
It's also a deconstruction of what being Batman would lead to. The members of the Bat-Family have washed their hands of him, Terry's relationship with Bruce even becomes strained due to Terry barely able to cope with being Batman, and Bruce is going to end up dying alone.
Moral Orel deconstructs The Moral Substitute but presenting a culture where ALL MEDIA are Christian fundamentalist propaganda, and showing just how messed up and disturbing said culture would be.
The Young Justice episode "Disordered" deals the aftermath of a traumatic mission, with the cast of young heroes attending therapy in order to deal with the horrible things they witnessed. The ensuing interviews reveal the pressure the kids are under and ends with Robin deciding that he no longer wants to be Batman.
Later episodes try to convey that being a teen superhero is not all fun and games, as we learn that Aquagirl, Jason Todd, and the previous Blue Beetle have all been killed in action during the five year Time Skip between seasons one and two. Upon this revelation, the line between superheroes and Child Soldiers begins to blur even more.
The episode of The Powerpuff Girls about them moving to "Citysville" deals with what would happen if their brand of heroics was applied to a real life city.
South Park, as well as deconstructing everything else on the planet, has a fine line in deconstructing itself. In "Kenny Dies", the Running Gag character they had killed over seventy times already gets a terminal disease and slowly expires while Stan and Kyle react with utterly realistic grief and despair.
"You're Getting Old" portrays Stan Marsh and his parents as completely fed up with the insane events constantly creeping in their daily life, along with Status Quo Is God. Randy, somehow an adult Sixth Ranger to the children, is forced to admit how immature that makes him when he cling to whatever awful next big thing comes out in an attempt to look cool and relevant; Sharon has this speech:
"I'm unhappy too. We both are, obviously. How much longer can we keep doing this? It's like, the same shit just happens over and over and, then in a week it just all resets until- it happens again. Every week it's kind of the same story in a different way but it, it just keeps getting more and more ridiculous."
... and Stan himself gets depressed as he grow out of his childish hobbies before his friends, without finding anything else to enjoy, and becomes "a cynical asshole" who literally experiences anything as "shitty". At the end of the episode, he has taken up drinking to cope with his depression, but as he hides it, to everybody else it seems like nothing has changed.
Also, this speech from Craig Tucker, one of the boys' classmate, in "Pandemic":
"Do you guys know why nobody else at school likes hanging out with you? Because you're always doing stuff like this. You're always coming up with some stupid idea to do something, and then it backfires, and then you end up in some foreign country, or in outer space or something. That's why no one likes hanging out with you guys."
The Jimmy Neutronmovie deconstructs the "no parents would be great" trope by having difficulties pop up the very next day. A girl gets injured, everyone gets chronically lonely, and people get sick from eating nothing but bad food.
"It's Oppo", a student film made by Cal Arts student Tyler Chen, deconstructs Nick Jr., as well as preschool television programs and morally unscrupulous media companies in general. Watch it [NSFW]: [http://vimeo.com/11573607]
In Undergrads, college dorm life is deconstructed to counter its inspiration Animal House; Rocko's Fratboy behavior is looked down on heavily by his frat brothers, who view him as a source of grief. Nitz' everyman status really puts only a grade above Gimpy, the resident Hikikomori of the 4 of them.
Transformers Animated is a deconstruction of the whole Autobot-Decepticon War. Things ain't so black and white as before, in fact the Autobots' leadership is flawed and somewhat corrupt, with one higly racist, incompetent, cowardly jerkass general on it, who only is amongst the High Command because he blames his mistakes on Optimus Prime, whose status as All-Loving Hero makes him somewhat of a push-over, and its leader is ready to commit dirty tricks to defeat the Decepticons. The Decepticons however, are as much the monsters they were in G1, and though this time Megatron's pragmatic enough to blast Starscream's ass any time he tries to overthrow him. Starscream only survives thanks to the Allspark piece on his head. Without it he would have died right from the start. Then comes the seasonthree...
Then The Legend of Korra goes further into deconstruction. It shows the rifts that could develop from a society of people with the ability to control the elements. While in The Last Airbender, people were generally too busy with the war to worry about discrimination of benders or non benders, during the relatively peaceful time that Korra takes place in tensions run high, resulting in things like curfews for non-benders and an anti-bending villain that spreads hate and fear against benders.
Book 2 goes even further by showing just how mentally fucked up The Hero could become from dealing with insane stuff like this all the time whilst being told by her mentor and allies that they're doing things she doesn't like "for her own good". Korra ends up developing some serious trust and anger issues and finds herself increasingly stressed out by the constant battles, betrayals, and reveals. Then there's Unalaq, who shows how much of an insane Knight TemplarThe Mentor could end up being in his attempts to do what he thinks is right and his attempts to sway and use Korra. He's basically Obi-Wan Kenobi played as a villain.