In episode 16 of Bodacious Space Pirates, pirate captain Marika has members of the Girl's Yacht Club help out on her ship, the Bentenmaru, while the regular crew is stuck in quarantine due to a virus they got in an earlier episode. When they raid a ship, the girls all show up in various cosplay costumes. Marika chuckles nervously throughout the entire "raid", but the guests on the ship don't seem to mind the costumes overall.
In Genshiken this is Ohno's hobby, while Tanaka's is costume designer for Cosplay. She often wears his creations for the club and to conventions. In Genshiken 2 they finally officially start dating, thus creating the dream Otaku couple.
In Genesis of Aquarion there is an episode called "Cosplay for the Soul" where Fudou has all the Element Users dress and act as each other to great (and hilarious) effect.
Persona 4: The Animation has Nanako doing a cosplay so convincing that she fools some kids into thinking she's the real Loveline (an in-universe, fictional, magical girl detective).
Spider Jerusalem at one point raids a religious convention while cosplaying as Jesus.
In one Freaks and Geeks episode, three of the guys dress up for a science fiction convention.
In season five of Supernatural Sam and Dean meet people cosplaying as them.note There's a series of novels In-Universe called Supernatural that is written by a prophet who writes the books based on what he sees in his visions. They're understandably creeped out by it.
And that's before they find out that the Sam and Dean cosplayers they interacted with throughout the episode are a couple.
In one episode they all dress like The Flash for Penny's Halloween episode.
They go as the Justice League team for the comic book store's New Year's Eve costume party, with Penny as Wonder Woman and Penny's then-boyfriend Zack as Superman.
The episode "The Barkersfield expedition" opens with Sheldon steaming his Data cosplay and Leonard having to borrow make up from his girlfriend for his. The A plot of the episode actually revolves around the guys getting stranded in the desert after pulling over on the way to ComicCon to do a full cosplay photo shoot. Leonard was dressed as Captain Picard, Raj as Worf and Howard as a Borg. They looked awesome.
In one episode, the girls decide to go to Disney land and they buy Disney Princess line-up with costume, make-up, hairdo... The only problem was that they all wanted to be Cinderella. Bernadette claimed it was her idea and that she was a driver, so she won. Penny was Aurora and Amy Snow White. Howard and Leonard really fancied their girlfriends in their outfits.
In the Charmed episode "All Halliwell's Eve" Phoebe cosplayed as Elvira and Piper cosplayed as Glinda. They didn't get to keep the costumes for long however as they were sent back in time to 18th century Virginia.
Castle: Castle, his daughter Alexis and Beckett have histories as cosplayers. Castle has dressed as Edgar Allan Poe, Space Cowboy and a Steampunk soldier on the show. Alexis dressed as a scantily-clad alien assassin at a sci-fi convention (much to Castle's chagrin). Beckett once dressed as a character from a short-lived Star TrekExpy called "Nebula 9" and also dressed in that costume again for Castle (adding a rubber fright mask to freak him out). Also during their teens, both Castle and Beckett dressed as Gene Simmons for Halloween.
Only Fools And Horses: As well as the famous "Batman and Robin" scene in "Heroes and Villains, outside the show there are a number of grown men who have acquired Robin Reliants and been Del Boy for various purposes, usually charity-related.
Trish Stratus and Mickie James's famous feud eventually had the two of them cosplaying as each other. It started with Mickie dressing as Trish for Halloween. After she won the title she began to appear as Trish with her music and wearing her gear. And then Trish did the reverse. Boy were people confused.
Litchi Faye-Ling of BlazBlue has a cosplay fetish that comes out when she's had too much sake, and whatever cute girl in arm's reach is usually subjected to it. So far, Noel and Tsubaki were victimized - Noel was coerced with playtime with Lao Jiu, while Tsubaki was a bit more cooperative... but just a bit. According to Arcade commentary, however, Makoto could be next...
However it turns out that Litchi's next 'subject' is Bullet after being dragged by the previous cosplay 'victim' to her clinic.
Litchi herself is a pretty popular subject to be cosplayed as in real life.
Fans! naturally gets into this on occasion. Notably Will has been known to dress as a Klingon.
One of the early Hijinks Ensue strips involves Josh's (real-life) cosplay as Kratos netting him Internet notoriety. His response is to create the most awesome costume ever created (this, sadly, did not also happen in real life).
Andrew Hussie of Homestuck fame likes to appear in the comic cosplaying one of his characters, usually one who's important at the time. In the story there's:
The Closing Credits Sequence of Daria features the characters in various alternate costumes. Most of the time, the costumes are generic an inspecific, like a cheerleader or a business woman, but occasionally they make specific references like Brittany dressed as Edward Scissorhands.
When the cast of Futurama goes to Comic Con 3010, they take part in the costume contest, with some of the contestants dressed as characters from the very show they're on. Lrr tries to invade Earth during the contest, but is dismissed as just another guy in a costume. The winner, by the way, is Bender, who dresses as "every nerd's fantasy", Leela.