Used in The Simpsons comic book. After Working on the Chain Gang, Sideshow Bob and Bart escape, chained together at the ankle. And while Bob tries to kill his long-time nemesis, Bart is Genre Savvy enough to point out that if Bob kills him while they're chained together, he'll have to drag Bart's body around as dead weight, and he'll be caught for sure. This forces Bob to keep Bart alive until he can break the chain.
Piper and Trickster, a pair of semi-reformed DC Comics supervillains, were handcuffed together after being arrested for complicity in the death of Flash. They escaped, but were unable to remove the handcuffs. The twist is that Piper is gay, and Trickster is, well, slightly homophobic.
Slightly? Constantly making gay jokes is more like it. Near the end of the storyline, it seems like it's going to become Canon Ho Yay just before Trickster does a Heroic Sacrifice and jumps in front of a bullet aimed for Piper. Poor Piper then drags Trickster's body around with him for days for before giving in to necessity and cutting the corpse's hand off.
Spencer Smythe was a Spider-Man villain, who was hired by J. Jonah Jameson to create robots to catch Spider-Man. When he got fatal radiation poisoning because of his work, he blamed both Jameson and Spider-Man, and handcuffed the two of them together with a bomb scheduled to detonate in 24 hours.
The Metal Men (except Tin) were once bound with a giant chain by evil robots. The chain is impossible to escape, even with their shapeshifting powers, as it expands and contracts with their every movement. Doc Magnus is especially unhappy to be chained to Platinum, as she's pretty much obsessed with him.
A chainless variant appeared in Thunderbolts, when Hawkeye, Plant Man, Headlok, and Cottonmouth escape from a prison truck. They're forced to stay very close to one another because of the bracelets on their arms, which will explode if they get a certain distance from one another. Cottonmouth, who is cannibalistic and part snake, tries to get around this at one point by killing the others as they slept, then chewing their arms off. Don't worry, he got caught in the act before anybody got hurt.