The hero is the antagonist, a Smug Super, Jerk Jock womanizer who believes that, because he is superpowerful, he's better than everyone else and is only too happy to display it. He further believes that only people who are like him can be heroic, and anyone who's nerdy or unpopular is a potential supervillain. It's strongly implied that this behavior is what drives people like the villain to become evil in the first place.
The Love Interest is a genuinely good person whom the villain wishes to impress with his evil deeds, failing to realize that she's very unlikely to actually respect that. She gets caught in the crossfire between the two, ends up ignored as they fight their climactic battle over her, and dies tragically as a result.
The Nigh Invulnerable super hero is only brave because he's never had to experience pain in his life. When he does, he has a Heroic BSOD over it.
It can actually be seen as a deconstruction of musical shows, because most musical shows have a positive outlook from beginning to end especially in regards to the lyrics of their songs. Dr. Horrible's got an awful lot of negative in most of the lyrics, even when attempting to be positive.
This website deconstructs the Cthulhu Mythos, specifically the Necronomicon. In essense it asks "what if it was a real book?" and builds from there, by looking for paralels between Judeo-Christian tradition and the Cthulhu Mythos (The Old Ones = The Giants from Genesis), it creates the content of the book, it then asks "what kind of person would write about such things in 730 AD?", thus Abdul Alhazred is what the Koran calls a "Sabian" and what western biblical scholars call a "Gnostic" a person with religous veiws related too, but radically different from mainstream Christianity, Islam and Judaism. It then builds a comprehesive history of how it got from the middle east and into the hands of western Occultists, and finally makes the assumption that while, yes Lovecraft wrote about it, he got only the name and the the author correct, having never read the book itself.
Stardestroyer.net, as mentioned above in Fan Fic, deconstructs the seemingly utopian Star Trek universe, pointing out holes.
Sailor Nothing loves showing just how jarringly, horrifically, nightmarishly different the characters' lives are from Magical Girl anime. Several of them even watch an exaggerated, stereotypical version of such shows; the main character actually watches it to escape her life.
Red vs. Blue: The Blood Gulch Chronicles takes many first person shooter tropes and twists them. Everything from capture the flag, to why there are two bases in the middle of a box canyon with no strategic value, and Respawn. Interestingly, the new series called Reconstruction is a deconstruction of the parodic nature of The Blood Gulch Chronicles.Caboose is tied up in the brig due to his self destructive tendencies. Grif and Simmons face the firing squad after selling all the ammo to the Blue team. The reason that all the red and blue conflicts were pointless squabbling over an equally pointless flag and base is revealed to be a conspiracy by command. However, since that is a deconstruction of a deconstruction, arguably that makes it a Reconstruction as all the video game tropes are being put back together.
The SCP Foundation Wiki, although beginning as a creepypasta site, has largely evolved into a deconstruction on the Urban Fantasy genre, depicting a shadowy organization entirely devoted to capturing and imprisoning all of those magicians, psychics, and mystic artifacts that populate said settings, to maintain the status quo. It is made abundantly clear that this is for humanity's own good.
Furry Fandom works frequently portray an entire world as furry. I Wish I Was Furry! shows what would happen if we woke up one day and the world actually was furry. The main character is even a human furry fan, like is typical for transformation stories. And a plushophile. (It's exactly what it sounds like.) A furryized world, as it happens, is dark and brutal. "Nature, red in tooth and claw" and all that.
This video from The Onion sends up the idea of video games becoming progressively more realistic by taking it to a logically deconstructive extreme with a "ultra realistic Call of Duty: Modern Warfare 3". It mostly involves sitting around and waiting.
The Whateley Universe is a deceonstruction of the classic superhero/supervillain tropes, with mutants who have to obey real physical laws, some supervillains like Dr. Diabolik who are pretty far from the classic villain, and even some supers who are far from the classic hero.
This video is a deconstruction of Pokémon. Yes, Pokémon. It is mostly played for laughs but there is a point about half-way through where Pikachu is bleeding as he's strangled by a Bulbasaur and it's played straight.
The Onion's Sex House series does this quite brutally to Immoral Reality Shows. Not only are the contestants much deeper and complex people than the shallow stereotypes the show desperately try to portray them as, the producers' "indicatives" to cut corners on the budget and ensure sex and drama in order to get the precious high ratings rolling in, soon starts to take a massive toll on their sanity and health.