Archie and Mr. Weatherbee in one issue switch bodies due to screwing around with one of Dilton's machines. It only lasts for a day, but that's well long enough for Archie to screw up Mr. Weatherbee's speech and The Bee to make Veronica furious at ol' Arch.
Speaking of Veronica, one issue of her own book featured a mystical pendant that swapped her with her own mother for a day. The two need to attend a fancy party together, and predictable shenanigans ensue. After that, the two just decide to wait it out, and pass the time with card games long into the night.
The crossover comic Harley & Ivy Meet Betty & Veronica involves Harley and Ivy swapping bodies with Betty and Veronica respectively, due to magical spells by Sabrina and Zatanna.
In Blake and Mortimer, Mortimer and Olrik switch bodies due to the latter double-crossing the former at the end of one issue. The reader is kept in the dark for the rest of the album and most of the next one. Olrik manages to fool all of Mortimer's associates for some time through a mixture of feigning partial amnesia and illness, and superb acting ability. However, given that Mortimer in Olrik's body is able to convince Blake of such a fantastic story fairly easily, it probably wasn't all that good.
Adam Warren's Amerimanga version of the Dirty Pair do this to themselves on purpose during the "Run from the Future" miniseries.
During the Eighth Doctor's tenure in Doctor Who Magazine, companion Izzy Sinclair and alien princess Destrii swap places, which becomes a serious problem when Destrii gets herself killed, to Izzy's horror. After spending some time as Destrii, Izzy gets captured by the people Destrii was running from. The Doctor, not far behind, returns to the planet where the swap took place and realizes Destrii isn't dead - she just got caught by the local species, and manages to fetch her and undo the swap.
A variant occurs in Double Jumpers. The development team working on Dungeon Lords 2 ends up swapping personalities with their programmed in-game avatars. Now they need to figure out how to get home while the characters in the game are running around in their bodies.
During Fred Hembeck Destroys the Marvel Universe, Crackers (the comic's version of The Grim Reaper) decides to switch the minds of Prince Namor the Submariner and Zzzax the Living Dynamo, resulting in Namor getting zapped to death by a electric outlet and Zzzax diving into a tub of water.
Issue 21 of the Invader Zim (Oni) comic series is built around this trope as an accident involving GIR, pudding, and a mind-swap machine causes Zim to switch bodies with Gaz, and Dib with GIR. The Mind Is a Plaything of the Body is, for the most part, in full effect — Gaz gains Zim's drive to Take Over the World while Zim becomes apathetic and game-obsessed, and Dib is ultimately rendered insane by the information in GIR's robot brain. GIR himself, meanwhile, doesn't change, and in fact doesn't even seem aware of what's happened.
Iznogoud: In "Chop and Change", a wizard invents a magic bowl: whenever two people drink consecutively from it, they exchange souls. Hilarity Ensues when this new invention gets tested by several patrons in an inn, just for fun. One of the catches is that it doesn't have to be actually people who drink: animals count too. (The wizard himself ends up in the body of a parrot.) Or even inanimate objects, for that matter.
A variant occurs in Safe Havens: Samantha and Dave accidentally drank DNA samples the dodos had left out instead of their drinks, and ended up turning into each other. The night before their wedding, no less.
One story in Wally Wood's Sally Forth had Sally swap bodies with a Killer Gorilla, as a prelude to a King Kong parody.
Papa Smurf does this with Gargamel in The Smurfs comic book story "Smurf Vs. Smurf" (and the Animated Adaptation version of "Romeo And Smurfette") in order to get the Smurfs to stop fighting with each other — in the comic book story, over the use of the word "smurf" in compounded words and phrases (or however the language war between the Smurfs is depicted in non-English versions); in the cartoon episode, to end a village-wide Ship-to-Ship Combat between Hefty and Handy over Smurfette.
In Super Sonic Special #12, Sonic and Knuckles switch bodies thanks to a scheming Dimitri and fake Robotnik, in order to blackmail them into getting the Master Chaos Emerald.
Happened once in Issue #37 of the Sonic X comic, in which Sonic and Dr Eggman switched bodies. Truth be told though, neither took real advantage of it, despite the cover suggesting more heinous actions by Eggman (in Sonic's body). Eggman in Sonic's body is unable to control Sonic's speed, while Sonic in Eggman's body has a hard time driving the Eggmobile. The story is resolved when the two use the ray Eggman used to swap their bodies to swap back. Eggman's comedy relief henchmen, Decoe and Bocoe tie up Eggman in the end, believing he is still Sonic, and interrogate him.
One Uncle Scrooge comic book had Magica swap bodies with Scrooge in order to steal his number one dime. Of course Scrooge is then able to access Magica's own hoard of magic tricks and use them against her.
. Rory doesn't care what Amy looks like.