An Applegeeks arc involves Alice switching bodies with a megalomaniacal little girl.
A one shot villain in Arthur, King of Time and Space restrains Arthur, gloats about becoming high king, pulls the switch ... and then realises that now he's the one in the restraints.
An NSFWnote Though not explicitly showing naughty bits, except maybe nipples comic by Ian Samson involves two lovers swapping bodies to teach each other what pleases them the most (which in her case, involves Wall Bang Her).
Another simulated instance happens when a haywire Magic Mirror misfires at a party, transforming everyone present (except Tedd and Diane) into someone else. These transformations are more thorough than usual, meaning Grace gets stuck with Tedd's bad eyesight and Nanase has to deal with Grace's Bizarre Alien Senses.
In Girly, there is an arc where many primary and secondary characters get switched around due to a "fist-powered" ray.
One of Lamerix's inventions in Jix caused Lauren and Jix/Lamerix/Remula (all three of Remula's personalities) to switch. The trio caused Lauren to break her arm as they were not used to walking without a tail.
The comic Lady Valiant has superhero fanboy Tom switch bodies with the titular hero after being caught in the crossfire of a fight, later learning that her secret identity is that of his homeroom teacher's. While she remains in a coma in his body, he tries to keep her life running with his best friend as the only person aware of the switch. Barring dressing in a more provocative manner once for class and being more aware of his new body, Tom is more interested in goofing off, testing his new powers and making notes out of them and needlessly spending Lady Valiant's admittedly large amount of money than anything else. At the very least, he does his best to keep her life intact as much as possible, moreso in terms of being a good superhero than being a teacher. Later developments Lady Valiant herself soon reawakens from her coma and regains some of her powers while in Tom's body and can even transform it female in turn.
In L's Empire, Void and Gemininman end up in each other's bodies the second time Spearhead is defused, due to Present!Pix's inexperience with his fusion powers. Coincidentally, the page that they swapped went up on a Friday.
Joked about in Questionable Content, where Hannelore thinks this is happening because she dreamed about it.
In Rain Burn the volcano dragon Brand and quetz Lady Saida accidentally switch bodies while trying to recover Brand's wings from the quetz queen. Their Kitsune cohort Roko is even less fortunate, winding up in a balloon animal.
In Sidekick Girl, the eponymous character gets switched with her useless but decorative boss and immediately complains about the cliché.
In Tales of Gnosis College, Willie and the lady professor he does work study for achieve a temporary and apparently accidental Freaky Friday Flip through an experiment with hypnosis and drugs. It leads to a torrid example of Professionals Do It on Desks.
Tales of Greed: "Calling" involves a phone that can swap the bodies of the caller and the recipient. The protagonist uses it to get back at his bullies and to date girls with handsome boyfriends, but he eventually winds up in the body of a serial killer with two murderous split personalities.
In a three-partWhomp! arc, Ronnie and Agrias experience this as a result of a Bungled Suicide. Ronnie still tries to go through with his original plan, only now it's closer to murder.
In "What's my age again?", this gets a little more complicated. When Anne uses the amulet that turns her older brother Evan into Lilly, she sneezes during the spell, causing Evan's mind in Lilly's body and vice versa. Like in Birdy the Mighty, Lilly and Evan are in the same body, but they are completely different people.
Wright as Rayne has a one-sided version of this. Vigilante Alex Rayne is forced to inhabit the body of teenage girl Dorothy Wright, but Wright's mind is in some kind of stasis.
Your Throne is built around this trope. Medea, who used to be engaged to the crown prince, switches bodies with Psyche, who is currently engaged to the crown prince. The switch takes place on the yearly day of prayer, and appears to be an act of God in response to Medea's prayer that He give her everything that Psyche has. She is alarmed to discover that Psyche's life was not nearly as ideal as it seemed.