The Noob is a very insightful parody of MMORPGs and the people that play them.
Super Megatopia is a cheesecake laiden parody of every superhero in existence. Highlights include Ferret Man (a combination expy of Batman and The Punisher — Oh, Crap!), Buxom Gal (an expy of Power Girl, right down to the costume, except Buxom Gal's powers are tied to her ever increasing bust size), Avatar (she's a god/dess! She doesn't know which one she is at any given time, but she has alien technology to help her prove her point).
In addition, "Crushed: The Doomed Kitty Adventures" parodies sword-and-sorcery fantasy games in general, but on-line RPG gaming in particular (such as the Temple of Infinite Lives and Crushed having to trek back to her body to retrieve her gear).
Concerned: The Half-Life and Death of Gordon Frohman, is an affectionate parody of Half-Life 2, as the title suggests.
Homestuck continues the trend with the notorious Inventory Management Puzzles. Later in the story, it becomes difficult to tell the difference between video game parody and actual plot elements. Also, as the page quote indicates, it likes to parody the hell out of individual fictional works like Con Air.
Radiant Dumb is an affectionate parody of Fire Emblem and its various game mechanics. Occasionally, it pokes fun at the story of Radiant Dawn and Path of Radiance.
Living with Insanity sometimes goes this route, such as the Talent Scouting arc where David attempts to kidnap Lar De Souza of Least I Could Do and Looking for Group. While making jokes about him and Ryan Sohmer, the arc is much more a loving tribute and Herbert has stated he has a lot of respect for the pair and their work. However, Paul does sort of ruin it by not even bothering to draw them to look anything like the real people.
Girl Genius parodies pulp 1940s serials, old-school science fiction, and every mad scientist trope in the book (the main characters all suffer from a trait which causes both madness and scientific genius ... and by "suffer", we mean they enjoy every minute of it.)
Looking For Group started as a parody of World of Warcraft, but eventually turned into a parody of the High Fantasy/MMORPG genre as a whole.
Voodoo Walrus reveled in this in introducing an entire team of overly muscled, gun toting mercenaries ala the comic anti-heroes of the late 80's and early 90's. The overuse of pouches and loud colors might suggest poking fun at Rob Liefeld's creations.
The cast of Times Like This occasionally do this, discussing what could've happened in Star Wars; or Gilligan's Island; or various commercials redone with historical figures. They even re-enacted the opening to a TV show.
WelcomeToHereafter does this an arc with the sunism church and Christian/Jewish dogma — Jesus even lampshades it. What makes even funnier is that all (real) religions get a comedy treatment.