The Case of Identity Switch features Dean Winchester (Supernatural) and Sherlock Holmes (Sherlock) swapping bodies when Dean touches a cursed chalice during a case. This results in an interesting side-effect where Dean finds himself capable of making deductive leaps in Sherlock's usual style, which Castiel later explains as the result of Sherlock's body retaining its intellectual potential; Sherlock-in-Dean is still capable of his usual deductions, but it requires more concentration as he's relying on memory and Dean isn't capable of thinking as fast as Sherlock is used to.
Child of the Storm: In Ghosts of the Past, this happens to a number of characters in chapter 2. The circumstances, however, mean that this is uniquely played for horror rather than comedy.
Halloween Unspectacular: The fifth Unpsectacular has a mini-arc centered around this: Plankton tries to use a pair of special socks to switch bodies with Mr. Krabs in order to get the Krabby Patty formula, but Dipper and Wendy end up accidentally using them instead. It also features a reference to the Gravity Fallsepisode that used the same plot, with Dipper's reaction to this being along the lines of Oh, No... Not Again!
Of Quirks, Dwarves, One For All and Arkenstone: Izuku Midoriya and Bilbo Baggins swap bodies every few days. After spending the first few sessions freaking out about this, the two realize that they could communicate with each other by leaving notes in their respective rooms for the other to find in a manner akin to the events of Your Name, heavily influencing each other's lives for better or worse. In addition, the effects of physical exertion are shared between them, which leads Izuku and Bilbo to share bodybuilding duties while they're in each other's bodies, allowing Izuku to finish his training to become One For All's vessel a week early and making Bilbo a very muscular hobbit.
Superman: Okay, Des. Last time we met, you put me through a little teaching session. You held me back from solving some problems that you said people could solve themselves, that you said they needed to solve themselves. So. You're the one who played Body Snatcher with both of us?
Doki Doki Club Meetings has MC's mod from Season 2, fittingly titled "Obligatory Body Swap Episode". In it, the Literature Club end up in each others' bodies due to a glitch in the simulation. Uniquely, Monika is actually capable of undoing the body swap quite easily, but the rest of the club decides to stay switched for another day because they hadn't learned any valuable life lessons yet.
Family Guy Fanon: The adaption of "Fast Times at Buddy Cianci Jr. High" features a three-person body swap, with Peter, Randall Fargus and Chris switching bodies through Fargus' body-swap machine, as Fargus was planning on showing it off at a Science Expo and needed data.
In the Flesh is essentially a sequel to "Out of Their Minds", where Moya is attacked by an alien race who have salvaged the ship from the original attack, except that this time only four of the crew are switched as the rest were away when Moya was attacked. As a result, not only are the crew forced to depend on Pilot for their rescue when he is transferred into Aeryn's body while the rest of the crew are captured after they return to Moya, but they also face a potential time limit as Chiana has been switched with Moya, creating the risk that Chiana’s body and mind will suffer permanent damage from trying to host Moya's soul/cope with the scale of input from Moya's body, which could kill both of them if left for too long.
Fate/Stay Night: Unlimited Abridged Works: The sixth episode has Caster switching the bodies between Master and Servants, such as Saber with Shirou and Archer with Rin, to make them easier to defeat (Sakura and Lancer also swapped bodies due to their partners being killed)
Elsa and Anna: Chapter 17 and 18 have the two sisters being cursed by a witch to switch bodies with one another under the prophecy of discovering how the other lived. And it started during an argument where they express their jealousy for each other.
The Switch has Anna and Elsa switching bodies with each other after the two drank a mysterious bottle at the same time. Unfortunately, the Annual Royalty ball happens to arrive soon and with the queen being the host, Anna is forced to learn how to act like a proper queen for once.
The Switch Glitch: A magic e-mail chain letter causes an eccentric fangirl to swap bodies with Edward Elric himself (for the first quarter of the fic at least). Hilarity Ensues.
Absit Omen: Body Swap Day saw a fair chunk of Hogwarts' population randomly swapping bodies thanks to a breakfast-time prank. It wore off by dinner, leaving enough time for a few relationship revelations and a canceled Quidditch match.
Being Harry Potter: Draco Malfoy awakens in Harry Potter's body. However, this is a Zig-Zag of this trope, because the person in Malfoy's body isn't Harry at all...
A Walk In Your Shoes has Lily and James experience this in their seventh year at Hogwarts with a twist of the understanding of the other being a prerequisite of changing back to their original bodies.
JoJo's Freaky Friday: When Baron Zeppeli is demonstrating Life Magnet Overdrive to Speedwagon through a lettuce, a sudden and powerful sneeze causes Zeppeli to expel his life-force into Speedwagon while pulling the latter's life force into his body, essentially a makeshift Hamon body-swap. Then when Zeppeli is trying to guide Speedwagon into undoing the process with his body, the two are started by Erina's sudden arrival, causing Erina to end up in Zeppeli's body and Speedwagon to be in hers.
Me as You: In a desperate ploy to stop Gabriel reign of terror as Hawkmoth, Nooro desperately swaps his wielder's mind with Adrien so the latter can free the kwami from his father's orders. It works, but it's only after the order that Adrien reveals that he's Chat Noir, meaning Gabriel now has one of the two Miraculouses he desires.
Diaries of a Madman: Several of them occur over the course of the story. So far they've been used for revenge, a competition to see who can act the most like the other, or have been caused by Twilight messing up a spell.
Into the Blender: A MacGuffin causes the Mane Six plus Scootaloo and an OC to swap bodies while also affecting four other ponies in their vicinity. The goal is to retrieve the item in question and get everypony back to normal.
Princess Trixie Sparkle: The story's driving conflict is that Twilight is switched with Trixie, Spike is switched with Rainbow Dash, Applejack is switched with Fluttershy, and Rarity is switched with Pinkie Pie.
A Mile in His Shoes uses the "learning experience" part of this trope with Zoro and Sanji's rather opposite approaches to romance being contrasted to the benefit of both.
Manaphy and its attack Heart Swap is often the catalyst for these types of plots in Pokémon fanfiction. (And even some non-Pokémon fanfiction.) Manaphy is often responsible for swaps between trainers and their Pokémon, Ash or one or more of his companions (like here), or various characters in Pokémon Mystery Dungeon fanfics.
Happened three times from Sinnoh to Unova-1, first with Jane and Palkia, the second time with DS and Artemis and the third with Daisy and Pink. A weird variation of this also seemed to happen between Jane and Entei.
Happens yet again with Anom and Wolf, due to a Manaphy. Unlike the other examples, it's played as a more serious major plot point rather than a brief joke, and lasted for pretty much the whole Oblivia arc.
This later happened in Kalos when a particularly "playful" Obscuric being decided to swap Mezzo and Eskay's minds. This ended up causing a small amount of chaos, especially when the fix turned out to be a kiss.
Deziree, Psyche, and Pentigan end up switching bodies for a brief period during the Fiore portion of Ranger-2.
In His Shoes has Genius Bruiser Hiko and BishōnenFragile Speedster Kenshin swapping bodies during a sparring match and trying to avoid detection. Aoshi almost figures out what happened, detecting the switch but not realizing it wasn't an advanced training technique.
Prison Island Break has Eggman and Finitevus do this as a psychological experiment on Sonic and Scourge (based on several comic issues). They try to fake each other to avoid being beaten up. However Sonic rapidly tires of how unpopular and lonely he's become and wonders if this is what it's like to be Shadow. Even better, he gets Scourge's Heroin withdrawal symptoms and finds out how hard it really is to come off drugs. The sociopathic Scourge however doesn't decide that friends are wonderful, but rather tires of having to be nice to people he considers weak, longs for Heroin psychologically, and learns nothing long-term.
Lightning has Stan and Kenny switch bodies after being struck by lightning. This leads to them assembling Coon and Friends to go into Cthulhu's dimension to get him to undo the swap, as well as Stan learning the secret of Kenny's immortality.
Switch Body!!, a fan-dubbed comic originally by fragonana: Anya and Damian swap bodies, where Damina goes into the Forger household to keep appearances while Anya goes to the Eden College dorm. At the Forger home, Damian is surprised how loving and caring Loid and Yor are despite the fact that Anya gets low grades.
"Bodyswap", and it currently has over 8,000 fics. Do note however that this also encompasses the occasional Grand Theft Me. 