All-Cheering All the Time - A notable aversion. The four all have wildly different personalities; Alex treats the cheer squad as a glorious military unit.
Attention Deficit... Ooh, Shiny! - Alex seems to have a mild case of ADD, noticeable only when she tries to go off on one of her long-winded speeches and gets derailed.
Bavarian Fire Drill: After getting rid of the (male) principal, Agent 32 manages to convince a teacher and some students that she is the principal—no, not a new one, the same one as ever.
The Cuckoolander Was Right - Jo is frighteningly aware of a large number of things she shouldn't be aware of, and not just her past as "Colin." It borders on being some sort of psychic or oracle.
Empty Piles of Clothing - Alex leaves these behind when she (apparently) turns into a small fairy or bug in the middle of an assembly. Naturally, when she pops up later, she's in desperate need of clothing.
Gambit Pileup- The student assembly ends up being one of these, with a minimum of six different plans being set in motion (with some other people simply winging it).
Involuntary Shapeshifting - Aside from the original Gender Bender, 32 turns Alex into a minotaur for help during the invasion. Since then, she's prone to weird transformations during emotional duress, but she never recalls any of her episodes.
Recently, Alex went into a WOW expy world and summoned a demon. Not only was the demon a attractive woman (specifically stated as impossible to create), but said demon then makes out with Alex for what is hinted as a long time. Bonus points? Alex says that if she was going to do that again, to give her a heads up.
Possibly has something to do with the fact that she used to be a guy and has a few lingering feelings from that time?
Noodle Implements - Apparently there's a lot you can do with two geese, a roll of duct tape, twenty-three toothpicks and some sodium benzoate.
This is even parodied in a [[ guest comic]], when the artist speculates exactly what those things are used for, but can only come to the conclusion that it causes vague panic in most people.
Orphaned Series: Hasn't updated since July 15, 2011.
Overprotective Dad - played with here. Bonus for Alex beating him to the sandwich baggie line.
Paper-Thin Disguise - Agent 32, pretending to be principal O'Brian. Note that O'Brian was a rather unattractive old man, and Agent 32 is, well... not. And her disguise is to just flirt with whoever asks until they forget what they were asking about.
Parental Abandonment - Alex, who is shown spending Christmas Eve strumming her guitar alone (sniff) and even gets her allowance via direct deposit.
RetGone-Proof Memory - Jo still remembers being a boy. Subconsciously, Alex does, too, as evidenced by some of her dreams. Also, The Wotch established that the girls' parents know that they used to be boys.
That was more of an Author's Saving Throw, as people were calling out Anne for forcibly changing people against their will, so by saying that, it would be ok (as Cheer does make it clear while they were Jerk Jocks for the most of it they were still the same people) plus it gets mentioned in The Wotch.
Anne's Feminist Pride says that spells can bring forth or diminish personality traits, but can't change personality completely. Thus, the cheerleaders are basically the same people they always were; it's implied their Jerk Jock behavior in their old life was because they thought that's how jocks should act.
Rich Bitch - Alex and Lindsay. Averted in Alex's case (she funded the Cheerleaders' post-Gender Bender wardrobe binge out of her own pocket) and semi-averted in Lindsay, who isn't a Rich Bitch so much as completely clueless about the way common people live.
Running Gag - Several, but especially agent 32's tripping people while invisible.
Also the Noodle Implements, which have been mentioned by multiple characters.
"Miss O'Brien!" "Who?"
Scary Black Man (Bruce Camaro. A pretty cool dude, but he is a bodyguard and therefore "intimidating" is in the job description.)
Schedule Slip - Following the typical webcomic arc from two to three times a week in the beginning to once or twice a month more or less at random lately.
Tomboyish Name - Alex, Sam, and Jo, though ironically enough their girl names bear less relationship to their former male names (Aaron, Gene, and Colin) then Cher's does to her former male name of "Sonny".
Uncle Pennybags: Alex is secretly very rich, but hides all mention of it because she's not fond of her distant parents.
Unsound Effect - part of the Wotch tradition, with new levels including mysterious trip! and THAC 0'D!
Weirdness Censor - Lita's mother knows she used to be a boy but hasn't said anything because Lita seems much happier as a girl.
In fact, it's established in The Wotch that all the families know, it's just that none of them ever said anything to the girls themselves, possibly due to Miranda's influence.
Or because Lita's mom at least is either really accepting of things or a ditz.
Yandere - Agent 40, aka "That Grinning, Psychopathic Harlot", not that she tries to hide it.