DM of the Rings deconstructs Tabletop Games, especially of the fantasy variety. The Lord of the Rings was basically the Trope Codifier for Fantasy Literature, with an epic plot and massive, meticulously crafted backstory. For decades now Roleplaying Games have often been based on fantasy stories and set in fantasy worlds... but you know, the actual progression of a roleplaying game doesn't look a thing like a fantasy novel, certainly not a good one. DM of the Rings takes several familiar player archetypes and transplants them into LOTR, and it's a disaster. The GM needs to use Railroading on the players every step of the way. Left to their own devices, they would have killed the elves of Lorien for the loot. They also complain endlessly about the boredom of the story (there's nothing to fight but orcs over and over again and Eldritch Abominations like the balrog, which their characters don't have the slightest chance against) and the way all the battles and side missions are entirely irrelevant to the main plot.
The side story Magical Girl Mina can be considered a deconstruction (or possibly reconstruction) of the magical girl genre. Mina is far from stereotypical proto-MG and does not adhere to any of the expected cliches, tropes and quirks (despite Tsunami being explicitly instructed to scout those traits) but is smart and fit and very inquisitive about how magic works and can be used. On the other hand Mina never reacts to the weirdness "normally" (such as fleeing or avoiding the situation) but accepts it with cautious curiosity.
Erfworld is a world where Tabletop Strategy rules are literally true, such as citizens popping in fully grown and a defeated team being frozen in time until someone comes to try and kill them. The more the rules become clear, the creepier everything starts to become.
It also deconstructs the typical Strategist with Parson's reaction to the aftermath of the Battle For Gobwin Knob. Instead of being proud and/or relieved that he won the battle against impossible odds, he is horrified by the death and destruction he has caused, so much that he steps down as Chief Warlord in favor of Ansom.
The Pixel Art ComicKid Radd, while largely light in tone, presents a "video game characters living in videoland" scenario where it's a very real problem that many inhabitants are innately armed and know nothing but killing. They know why they were created, and they don't like it. The player character Radd goes from slacker to Determinator because he always had the latter's mindset, but started his days in a game under the player's control, so he had to learn initiative completely from the ground up. Upon being freed, Radd needed instructions to walk independently.
It's Walky! could arguably be seen as a deconstruction of the goofy 1980s cartoons creator David Willis is a fan of (mostly G.I. Joe and Transformers). Sure, it features a unique special forces group, SEMME (who were initially based on GI Joe) with an eccentric line up of operatives, who routinely foil the insane schemes of a Harmless Villain, but the eccentric operatives are soon revealed to be a bunch of dysfunctional screw-ups, and the Villain is in fact a Not-So-Harmless Villain.
Alternately, it's pardoying Ren and Stimpy's Adult Party Cartoon, which took place at about the same time. (And was a MUCH Darker and Edgier Ren and Stimpy)
Goblins: Life Through Their Eyes takes a good hard look at the Unfortunate Implications of labeling whole races Always Chaotic Evil. It portrays the titular goblins not as monsters but as people who live and love. It shows us that what Player Characters see as just an XP haul isn't so fun when you're the one they're killing to level up.
With engineering, it was criticized how dangerous it was to rely on unstable power supplies (in this case, anti-matter) to make your ship's hyperdrive run, how senseless and dangerous it is to have everything being run by one massive computer system instead of having different units assigned to different areas of the ship independently and how this can cause a security danger, and how having only voice recognition as a security measure for doors can be bypassed and exploited by having voice changing abilities (which the android in the crew possesses) and simply recording someone else's voice.
The entire premise behind Darths & Droids is that the Star Wars universe is the result of a group of Tabletop Gamers (including a 7 year old girl) making it up as they go along. It lends a whole new perspective to the storyline of the prequel trilogy. The entire mess on Naboo was the result of the Player Characters epically ruining a delicate, carefully constructed plan by going Off the Rails, and engaging in all the sins of The Real Man, The Munchkin, and The Loonie. Palpatine is actually a good guy overthrowing a corrupt regime, and trying to bring a semblance of stability to the republic. Darth Maul was just a Chaotic NeutralHired Gun who was only trying to work with the player characters, before they attacked him. To top it all off, some the most bizarre and unrealistic plot points, such as Naboo being governed by a 14 year old elected Queen exist because Jar Jar Binks is being played by a little girl.
In the Chapter 26 of the Spanish webcomic 5 Elementos, the author shows the effects of a civil war in a world inhabited by lots and lots of people with superpowers.
Misfile can be considered a broad deconstruction of the Gender BenderTransformation Comic, showing how much it would actually suck if you were transformed into the opposite gender and didn't have those kinds of tendencies to start with (the part frequently ignored by TG comic fans who wish something like that could happen to them). Ash is depicted like a real transgender teen would be (literally a boy trapped in a girl's body), with a realistic level of distress to not only the biological and social changes, but to also having the entire foundation of your world and personal identity ripped out from underneath you.
One could say that Sluggy Freelance is something of a deconstruction of what it's like to live in a Fantasy Kitchen Sink. Eventually, the amount of supernatural villains you piss off (and the infamy among the inhabitants of said Fantasy Kitchen Sink that you gain through your deeds) will reach such a critical mass that your entire life will be swallowed up in a never-ending, breakneck onslaught of attacks and reactions to your attempts to defend yourself from said attacks from grudge-holding demons, psychopaths, monsters, conspiracies, Eldritch Abominations, Artifacts of Doom, evil Mega Corps, etc., etc. Being a fairly early webcomic, this has been subjected to a measure of "Seinfeld" Is Unfunny.
Strong Female Protagonist: The superheroes start out as kids and teenagers who are exposed to some unexplained environmental phenomenon that gives them powers, and most of them start out with the best of intentions and a genuine, idealistic desire to make the world a better place. A few years later, they're all young adults and they realize that they haven't really made that much of a difference, and their powers can't really help them solve the world's problems. The main character is a Flying Brick who's coming to terms with the fact that being able to lift a car over her head doesn't equate to being able to actually fix anything. Her arch-nemesis, a classic Evil Genius supervillain, retires from the Bad Guy game when he finds it intellectually unfulfilling and, frankly, childish. A girl with a mutant Healing Factor decides that the only real way she can make a difference in the world is to become a living organ farm for the rest of her life. And nearly all of them are deeply traumatized from spending their formative years fighting crime and the forces of evil (one minor character points out that they were basically child soldiers).
Kubera is largely a deconstruction of shounen action comics, and The Hero's Journey-type fantasy in general. The heroine is an Idiot Hero because she wasn't allowed to go to school, and her Doomed Hometown was only destroyed because the sura didn't think it was worth the trouble to find the one person they wanted to kill and just obliterated the whole place. Her gruff mentor figure is actually rather abusive and completely ruins her sense of self-worth. The protagonist is thrust into the role of the hero but doesn't get any of the rewards, respect, or companionship that comes with it because most of the people around her are simply manipulating her for their own ends.
Shattered Starlight has started to show some of the realistic results of a Magical Girl lifestyle, especially after growing up, with Farrah showing some signs of PTSD and having trouble keeping a regular job, the team apparently having broken apart after some event hinted to have ended with a member dying, and the former team mentor is now near-constantly drunk.