Aborted Arc: One arc was a parody of Sky Captain and the World of Tomorrow, but the Artist cancels it a few strips in because it would take forever and the movie wasn't all that interesting to begin with. That, and he gave up trying to work out how to write strips without spoiling anything.
Author Avatar: There is not only Greg Dean in the comic, but also the Cartoonist, who is usually portrayed as a disembodied god. When he does appear in-strip, he looks like Greg but with slightly longer hair and different clothing.
Cerebus Syndrome: Completely averted despite being such a long-running series. Although it's had short story arcs, they're never serious, and has managed to stay funny without ever running out of material. (Except for a few comics where the creator has no ideas for a strip, which still end up being funny).
Well, the story arcs where Tony battles an FBI agent who wants Tony's tech for the U.S. government get kind of serious at times, but it's hard to worry that any major characters will die when you know that every one of them is based on a friend or relative of the creator.
Cliché Storm: An In-Universe example was done during a dimension-hopping adventure where they wound up in a world where "everything is a Sliders cliche!". Naturally, this involved their dimension-traveling device fizzling out, a doomsday scenario, joining and fighting a rag-tag resistance group led by a double of someone they knew, getting involved with and solving the world's problems and a last second escape. Well, almost all their problems.
Alt Dave: That's great, but what about the huge freaking asteroid about to hit the planet?!
Tony: Sorry, pal! You're on your own!
Closer to Earth: While this could always be said to have been the case between Liz and Greg, the comic has really started to abuse the use of this trope (and all that typically goes with it) in the last few years. Like, "Last season of Everybody Loves Raymond" abuse it. One could argue that Liz is, basically, a live-in Straight Man to Greg's wise guy, a role which used to be filled by Dave and Tony.
Though Liz does have her moments too, like when she and Greg went car-shopping ("NewBeetleNewBeetleNewBeetle!" "Maybe we should get a bigger car?" "NEW. BEETLE.")
Continuity Porn: This 2008 comic marks the beginning of an epic story arc that makes references to several past story arcs, including one that began in 2002.
Corruption of a Minor: Dave complains when Greg plays Diablo 2 with his newborn daughter Harper in his arms, but he insists that it teaches her important life lessons:
Greg: That's right, Harper, demons do gots to be slain!
Cut and Paste Comic: Most of the comics consist of the characters and backgrounds being cut and pasted with new dialogue put in. The creator sometimes makes a fuss about new backgrounds or objects.
One arc, mirroring Greg and Liz' real world house-hunting, had a strip in which the camera suddenly refused to follow the characters. Then a note floated down from the cartoonist, stating that due to the flurry of new backgrounds he's had to make recently, he had decided to go into a coma.
Fridge Brilliance: In-Universe: In one strip, Greg suggests that the graphic designer of the much-reviled Comic Sans font was actually a genius, because it's basically a huge flashing sign that screams "I'm incompetent and need the help of a graphic designer." Liz is stunned when she realizes that it makes perfect sense.
Humongous Mecha: The arc starting here, where Tony builds a Mechwarrior and his girlfriend is given Eva-00 when she gripes to the author, resulting in an East vs West throwdown. The 'Mech destroys the Eva's power cable, but it doesn't have any weapons capable of penetrating its defenses so the whole thing ends in a draw.
Internet Backdraft: In-Universe example: In one strip, Liz tries to get Greg into Doctor Who; he refuses, citing his addictive personality and saying he doesn't need another show to obsess over. The very next day's strip has him telling Liz he'll give it a shot, revealing that he got so many emails from fans telling him how great DW is that it overheated and melted his computer.
And more recently with an arc involving the first Final Fantasy.
No Fourth Wall: The cartoonist has physically appeared in the strip, and occasionally talks to the characters from outside the comic. The Plot Hole arc had Tony climbing through a plot hole into the real world.
Real Life Writes the Plot: A particularly bizarre, recursive example. Greg met his wife, Liz, through the forums; their marriage and her pregnancy with their first child have been part of the comic. It gets silly when, in-comic, Greg shows his child the comic. In short, Real Life wrote the plot of real life, which was then written into Real Life, which was shown in real life to the daughter who exists as a result of Real Life writing the plot of real life, which in turn wrote a strip in Real Life.
Tempting Fate: In one strip, Greg says he prefers Google+ to Facebook because it doesn't have any annoying things like people poking your or inviting you to Farmville. Dave immediately goes to his own computer and messages Greg, saying simply "*poke*".