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.
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.
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 and/or were overcompensating for their more "feminine" (sensitive) inner natures.
Implied nothing, in a wotch one shot comic 'Jo' expressed extreme hatred of how his male body and large 'football' hands made it difficult to do arts and crafts which he enjoyed, this was follwed by a ghostly image of his future girl sself hugging the boy sadly.
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.
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.