There are no literal chains in Double Arts—just the simple awareness that if Kiri lets go of her hand for more than a few seconds, Ellie will go into a horrific seizure and die. Needless to say, they are, for all practical purposes, just as good as chained together.
Although they were able to take advantage of it not being exactly the same in the first chapter to win a fight by switching hands to get an advantage.
In the Gintama anime, Hijikata and Okita are chained together at the neck with exploding collars as a parody of the Saw franchise. They spend the next few days foiling each other's attempts at escape.
Hijikata got handcuffed to Gintoki and had to request his help in taking down some bad guys. Hilarity Ensues.
In Seo Kouji's oneshot manga Half And Half, the male and female protagonists are both involved in an accident and die together. Then a rather generic Kami-Sama gives them a chance to live again, for 7 more days; the catch is that after the time limit, one of them must die again. They're forced to stay together until they decide, else they both die.
In a side story of Kamichama Karin, Karin and Kazune'smagic rings ends up stuck together, and by extension their hands. Instead of having to make excuses for cuffs, they have to avoid being seen with their hands stuck together or face the wrath of Kazune's Fangirls. This leads to some rather funny moments where Kazune has to go to the bathroom and where they have to change for gym. The latter leads to a Crowning Moment of Funny where their enemy walks in on them in a... compromising position.
Has happened a couple of times in Lupin III, when Zenigata actually manages to cuff Lupin. And quickly learns that the downside to cuffing yourself to Lupin, is that you are now cuffed to Lupin. And he isn't chained to anyone.
A Naruto filler episode recounts an instance where the original Team Kakashi faced a gang of thieves lead by Ninja Spiderman(the guy even webswings in one scene). Naruto and Sasuke wind up with their hands webbed together for the remainder of the flashback. During the Hilarity Ensues scene of trying to seperate themselves, they accidentally kiss... again.
Done in the Pokémon anime, in which Ash's Pikachu and Team Rocket's Meowth are tied together for an episode.
Also in the Pokémon Special manga with Blue's Ditto and Sabrina during a battle. Hilariously, Sabrina was furious to find out that they weren't even chained together at all.
In the manga as well as an episode of Princess Resurrection. Reiri and Riza, a vampire and a half-werewolf respectively, end up getting handcuffed together by Hime as she needs them for a rescue mission knowing full well they would object to it if they had to work together.
Having two characters chained together actually happens fairly often in Ranma ˝. Somewhat subverted in that they very seldom get along and generally find some way of using the other as the weighted end of a chained weapon.
Such as Ranma using P-chan as both a shield and blunt object in a Martial Arts Gymnastics match with Kodachi.
Sailor Moon: An attack by a Daimon handcuffs Sailor Moon and Sailor Uranus together for an episode. This serves as a plot device since they'd been at odds since they ran into each other and have avoided contact. Being stuck together helps each to understand how the other thinks.
In the manga Train Plus Train, average everynerd Reiichi Sakasuka ends up handcuffed to fugitive Arena Pendleton. The cuffs are indestructible, but time-released. They just had to wait 99 hours, which meant that Reiichi had to cancel all his plans and go on the run with her. This was just the beginning of the tension between them.
In Detective Conan, when Heiji Hattori and Kazuha Touyama were kids, they got handcuffed while playing with a pair that belonged to Heiji's policeman dad. They spent a whole a day like that, and when they were released Heiji kept an amulet made with a piece of said 'cuffs. Which would later become a Pocket Protector, and save Conan from being stabbed to death.