Abusive Parents — Jamie's parents. His dad is shown to be curt in Jamie's story, but nice and apologetic (or at least good at dealing with kids) in Alex's story. But then, he divorces Jamie's mom and more or less cuts Jamie out of his life when he leaves home. Oh and speaking of Jamie's mom....
This applies to a rather large amount of Khaos' forum members as well.
Art Shift / Art Evolution / Retcon — the artist has expressed dissatisfaction with the original versions, so the story has been re-written and redrawn from scratch chronologically from the beginning to the end of the current version.
Arson, Murder, and Jaywalking: When Charlie gets her own computer, her mother warns her to beware of pedophiles, never give out personal information, and avoid misogynistic websites.
Bi the Way — Definitely Nay and Charlie, possibly Steve (who's admitted he only calls himself bi because it sounds "less gay") and Murfs (who's so far only professed an attraction to Tom, and not most men - or at least not Jamie - but he's quite young and doesn't really seem to favor men over women).
Bilingual Bonus — Also counts as a Stealth Pun. Tom's birth name is "Maria" and "marimacho" is a Spanish equivalent of "tomboy". The "mari-" in it comes from "Maria".
Camp Gay — Mark, very much. Alex also picks up some mannerisms as he becomes interested in Tom; that part of him is "Inner Alex", who shouts inappropriate stuff in regular!Alex's ear.
Cast Full of Gay — Just look at that list above! The author can get a wee bit defensive about this at times, with the front page at one point saying "this comic contains an equal amount of straight and gay people, but... I only really write about the queer ones."
Specifically, Steve, Mark and Tom are gay, Amber is a lesbian, Nay and Charlie are bisexual, Alex has Single-Target Sexuality, and Jamie is straight.
Closet Key — A lot of the characters end up being this for each other.
Colour Coded Characters — Sort of. Every major character has their own colour theming (yellow, blue, red, purple, orange, brown, green, and cyan, respectively by chapter order), and it's evident on the title pages for their respective chapters, as well on other page elements for all strips within each chapter. As the comic itself is black and white though, it's rather less evident during the story.
Did They or Didn't They? — Steve and Mark the morning after they got drunk and slept naked in the same bed; Steve freaks out and has no memory of what happened, while Mark (who limps around for the next two days) both claims that they did have sex and that he doesn't remember anything. A clearer picture is painted in Mark's story: they tried, but failed because they were drunk and inexperienced—Mark remembered everything, but lied about it because Steve freaked out.
Easy Sex Change — Averted, as it just doesn't work that way. The two Transsexual characters have considered the operation, but they known it's a long, painful process, and the author also points this out in the FAQ.
Meanwhile, the non-surgical transition happens quite easily, which Tab admits to being a mistake due to not doing the full research while writing the script, and being unwilling to Retcon it out.
Erotic Dream / Homoerotic Dream — Amber had one of Nay, which made her realise her feelings. Steve also had several of Mark, but tried to fight them off with cold showers.
Fanservice — The "side stories", first featuring Mark and Steve having sex for the first (successful) time, the second detailing an intimate encounter between Nay and Amber, third dealing with an encounter between Tom and Murfs, also adressing the complications of transgender sexuality. The FAQ adresses this:
Why do your characters all fuck each other? Because I am a fan pandering whore who likes money. 
Irony: Jamie's terrified that he'll force himself on Charlie because of his background. Later in his story, Charlie comes inches away from forcing herself on him.
It's All About Me: Jamie's mother. Jamie even lampshades it by commenting that she only cares about herself and what she will get out of something. She's so selfish that she didn't even tell anyone about Jamie getting raped, nor tried to give him any medical help, for no other reason than to protect her own reputation.
Jerkass: Tom, to some. He's unwilling to give Jamie his chance with Charlie (albeit with some good reason) and he does dump Murfs out of nowhere. Worse, he flirts with Murfs while they're broken up (though he does seem remorseful when he's called out on it).
Karma Houdini — So far, Natalie and her friends, who look to be in the clear without ever receiving their come-uppance. There's also Jamie's mom who practices some seriously questionable parenting but hasn't received any retribution — yet.
My God, What Have I Done?: Charlie gets a moment of this during Jamie's story. After struggling to be intimate with him, due to the history of how he was sexually abused, she meets up with a girl that she can tell he's slept with. She does not take it very well. Specifically, she comes within inches of sexually assaulting him - only to pull back when she realises that her own insecurities about whether or not Jamie sees her as a "girl" are driving her to an insane panic and pushing her towards her own Moral Event Horizon. She realises that she could have done the very same thing as his rapist and ultimately spends the rest of his story full of guilt and regret for what she's done; even willing to completely swear off any kind of sex if it helps Jamie feel better.
My Greatest Failure: Tom is a wee bit protective of Charlie, after not being able to save her during the bully attack.
Open Minded Parent — Charlie's mother, and Tom's mother. Upon seeing Tom bring Alex back she tells Tom in Spanish to use condoms since he can still get pregnant. Parents in general seem to be this in the series.
Pair the Spares — When Mark and Amber were dating, they tried to set up Nay and Steve at a double date. Backfired, and resulted with both pairing up with their respective "spares".
Poor Communication Kills : During Jamie's story, Charlie's insecurities about whether or not he sees her as a real girl and envy towards the genetic girls he's slept with cause her to almost sexually assault him. As it turns out, Jamie did see her as a real girl. He was simply afraid of becoming intimate with her - someone he loves - because he considers himself too "tainted" to be worthy of her. In the end, the failure of both parties to properly communicate these issues until it's too late leads to Charlie spending the rest of Jamie's story disgusted with herself for almost crossing the same line as his rapist and Jamie realising that, if he doesn't seek professional help to conquer his demons, he's only going to make things worse for himself and Charlie.
Which doesn't even hold a candle to the guy who abused Jamie. The distortion as if from a child's point of view makes it all the more terribly realistic.
Straight Gay — Steve, who's only intersection with any stereotype is an enthusiasm for baking; granted, he claims to be bi, but even admitted to the audience that that was only because it "sounded less gay."
The Bad Guy Wins: Natalie and her gang successfully assault and hospitalize both Tom and Charlie. Natalie then threatens to attack Charlie again, possibly at her own home, if she doesn't leave town. Not only does she opt to flee but Tom follows her shortly thereafter.
Jamie's rapist is never caught, and as far as we know is continuing to live his life perfectly well.
Subverted when the comic finally gets around to his perspective—he's actually the most confident and self-aware in his sexual identity of the main cast. He objected to being called "gay" simply because he'd never met anyone—male or female—that he was particularly interested in, so it wasn't accurate.
Mark would have been a classic example except that no one except Steve and Alex seems to notice his typical campy mannerisms.
(In-Universe) Jamie is very homophobic (he's getting better), and starts dating Charlie, a transgirl. Tom, apparently without thinking about it, decides that this must mean he's gay and in denial. This implies that Charlie is male, something Tom, of all people, should know isn't true.
What the Hell, Hero? — Mark calls out Steve for punching Jamie after they both come out to to him and he doesn't take it well. Everyone else that doesn't like Jamie even seems to agree it wasn't a good idea to come out to him in public.