Alt Text: Most cartoons have a bonus panel, called the votey, that you see if you mouseover the red button at the bottom of the main cartoon. Called such because you used to have to vote for the comic in a poll about webcomics in order to see it.
Author Tract: Many strips savage organized religion, in particular Christianity. To be fair, Zach often pokes fun at atheism/agnosticism in the same breath. He's also not above taking a potshot at bothsimultaneously.
Back to Front: Done many times as a form of comedic reveal.
Bad Date: "Date Wars" is a bad date summarized in an actiony death-ray battle.
Bait and Switch: As said above, one of the comic's claims to fame is subverting the audiences expectations, or even double-subverting them. Taken to ridiculous extremes (to the point of self-parody) in this strip.
Birds of a Feather: Subverted in "Uncomfortable Truthasaurus". It's kinda cruel, but those two nerds who date each other? They want, like all people, someone hot and with better social status than themselves.
Bizarre Alien Biology: It makes giving the aliens one million children in exchange for their advanced medical knowledge a poor decision in hindsight.
Crapsack World: Where all doctors and lawyers are incompetent, all relationships are dysfunctional, and suicide and murder are apparently common pastimes. Also, the unicorns? Racists. In some cases though, the doctors are competent sociopaths, and the dysfunctional relationships work due to nightmare fetishism.
Good Angel, Bad Angel: In debating whether he should kill his own family, the man's bad angel kills them himself. Say what you will, but sociopathy is efficient.
A combination of twostrips plays creationism for laughs by invoking the idea that the theory about the earth moving around the sun rather than vice versa is only a theory. The first strip joke about creationists demanding to put "evolution is only a theory" stickes in biology textbooks. The next strip joke about a guy from the 13:th century demanding the same kind of stickers in astronomy textbooks.
In a much later strip, a character argues that history is only a theory. More specifically, he does no believe in "the theory of revolution": According to his religion, all states were created in their current form.
It Makes Sense in Context: Some of the panels and/or the dialogue in them can be really bizarre before you read the caption, or in some cases the bonus panel.
Long Runner. So you like the latest strip. You click to the one before. It has a big number in the URL. (2000 as of September 14, 2010.)Then the one before that. Big number minus one. Oh Crap.
One-Two Punchline: There's an entire bonus second-punchline panel accessible by hovering over a red button at the end of the strip.
Only Six Faces: Though in this case, it doesn't really matter.
Opposites Attract: Truthasaurus from "Uncomfortable Truthasaurus" explains you, kids, that this is a common misconception. Everyone wants someone hot and someone rich.
Having fun when parenting (on the expence of the kids). Among others, there are two specific routines:
Kid asks something, parent explains, kid applies explanation (or other parent asks "what did you mother/father teach you") — example: female reproduction is thematically named after puncuation http://www.smbc-comics.com/index.php?db=comics&id=2483#comic
Subverted Trope: Too many to count; half the strip's humor comes from doing this in a bizarre manner.
Double Subversion: Many, many gags involving something turning out to not be what you think it is, and then turning out to be what you thought it was after all.