A character has been shackled or put in handcuffs and upon being released they must rub their wrists. Somehow this not only stops the pain but removes all physical evidence that the character was chained up to begin with. In fiction land, having your hands tightly bound for long periods of time usually only causes mild discomfort.
In the Turnabout Gallows case of the Ace Attorney manga, Maya does this with her wrists after being momentarily trapped in a chair that restrains the people in it by their wrists, ankles, waist, upper arms and shoulders. This one is more justifiable than most examples given that Maya was only in the chair a few minutes and therefore would be sore but otherwise unharmed.
In Empath: The Luckiest Smurf, Empath and Polaris both have their wrist and ankle cuffs removed upon their release from Psychelia, but are never shown to rub their wrists or ankles afterwards. Apparently being in cuffs for a long time causes very little discomfort.
Films — Animation
Aladdin: The Genie does this when he is freed from the lamp. Aladdin himself does the same earlier in the movie when he was freed from prison in order to go find the Genie.
Disney's Robin Hood: Friar Tuck has been hanging from shackles for at least a few days, but upon release, five seconds of rubbing and presto!
Disney's Sleeping Beauty: Prince Phillip also does this when the good fairies release him.
Sinbad: Legend of the Seven Seas, after Proteus offers himself to be executed in place of Sinbad (should he fail to retrieve the Book of Peace), Sinbad's cuffs were released, he grasps one of his wrists.
In Dead Man's Chest, after Governor Swann is arrested, CutlerBeckett makes a deal with him, and, after he agrees, he takes off his shackles, after which Weatherby rubs his wrists, which are noticeably red and raw (and probably painful).
Jack in the third film, right after he's shoved into Beckett's cabin. (We don't actually see the cuffs before removal, but since he's a prisoner it's strongly implied he had 'em.)
In The Quick and the Dead, Cort is kept shackled between duels. Before his second round fight he can be seen ripping the cuffs of his shirt out of the bloody welts left on his wrists by the shackles.
Midnight Run: As Jack uncuffs the Duke on the train, the Duke says, "Thanks, 'cause they're starting to cut into my wrists." In fact, the actor Charles Grodin (who played Duke) has permanent scars resulting from the handcuffs he had to wear for most of the film.
City Of Fire: note 1987 Hong Kong action film, the inspiration for Reservoir Dogs Averted — the protagonist is seen limping down the street in pain after being hung suspended from handcuffs by his fellow officers.
Hot Shots! Part Deux: Lampshaded — a character has two fingers bound by the bad guys with a Chinese finger trap, when he is freed, he begins rubbing his wrists.
Avatar: Grace does this, after the first time Quaritch and his goons haul her out of the link.
No Country for Old Men: Decidedly not the case. The main antagonist (who begins the movie in handcuffs) and murders a deputy by strangling him with the handcuffs on his own wrists is later seen washing his torn, bloody wrists after the handcuffs are off. Although admittedly this is probably kind of an extreme example.
Averted in Yes-Man the two main characters are handcuffed in an airport by security. When the cuffs come off, they don't rub their wrists.
Played with in Friday the 13th (2009) reboot. A girl is chained to a small area and her legs and hands have grown weak over the past few days. She can barely walk when at first when she is freed. But after a few minutes she's completely in perfect shape again.
In Krull, the prince proves that he is the prince by using the master key to free the shackles from the escaped criminals. They remove their cuffs and rub their wrists.
In the first chapter of The Green Hornet Strikes Again!, Britt and Kato are captured and tied up by crooks. After they get free, both of them rub their wrists.
The Sting. Detective Snyder arrests Hooker and takes him to meet with Special Agent Polk of the F.B.I. Polk tells Snyder to take off Hooker's handcuffs and Hooker rubs his wrists after he does.
"The Bound Man" in Unknown2006 only rubs his wrists after having them untied despite complaining that "they turned blue", but the guy left hanging by one handcuff is visibly in great pain and it's stated that he'll almost certainly lose that hand.
Captain Danilo does this in romantic comedy The Merry Widow when taking the stand at his court martial. The queen, who was having an affair with him, had his handcuffs engraved "From Dolores to Danilo".
The second Protector of the Small book averts the trope. Lalassa was bound tightly by rope, not handcuffs, and left overnight. She could barely move after being untied - her rescuer had to massage her hands to get the blood moving, the dog took care of her ankles - and had pins and needles afterwards, as well as rope burn. The Provost's Dog books also justify this, since instead of handcuffs the Provost's Guard uses leather thongs to tie people up.
The Queen's Thief: Averted. Gen's wrists are badly injured by his time in shackles in Sounis' prison, and this becomes a problem on at least one occasion in the novel.
Averted in Gerald's Game. Not the "rub your wrists" part, that's still there; the "mild discomfort" part. Of course, slicing your own wrist so that the blood will provide enough lubrication to slip your hand through the cuff is a little more than "mild discomfort" for any setting.
Averted in Little Brother, after his wrists being zip-tied together for a few hours, Marcus can't feel his hands, nor move them, and his fingers are described as looking sausage-like.
Averted in Splinter Of The Minds Eye. Halla, after being bound upright for half of a day, can't stand on her own when cut loose.
Sort of averted in A Song of Ice and Fire books, where being tied up or chained up can be extremely painful, but also sort of played straight, since a couple of characters survive being restrained in ways (like being strung up dangling by their wrists for extended periods of time) that would probably kill them or at least permanently disable them in real life.
Live Action Television
Friends: Simultaneously subverted and lampshaded. Chandler's been handcuffed to a chair. Upon being released he does this. Rachel asks if it hurts. He responds that it doesn't, but people always do it in the movies.
In the pilot episode first time we see Kate, she's doing this. We don't find out why until the second part of the episode.
Averted with Jin. After spending awhile with one half of the handcuffs still on his wrist, it's started to leave marks. Sun notices and asks him to have Jack look at it.
In a later episode, when the Others have handcuffed Kate, Tom gives her aloe for the cuts and irritation on her wrists.
Even later on, when we see Richard in a flashback his wrists are a bloody, infected mess from being in handcuffs for several months.
iCarly: Spencer is arrested for causing a traffic jam with a large sign for iCarly. When the handcuffs are removed, he rubs his wrist and says he needs lotion. The cop who arrested him taunts him with cucumber melon lotion that he won't give up, since the sign malfunction to read "PEE ON CARL", and his name is Carl.
Averted in Merlin when Guinevere is captured and held in handcuffs for a day before being returned, she tries to lie to Merlin and say she was sick. Merlin immediately points out the marks on her wrists. They vanish after a few days, but that's another trope.
Averted in an episode of Murdoch Mysteries in which Det. Murdoch is abducted and tied up; the episode ends (some time later) with a scene between Murdoch and Dr. Ogden as she applies an ice pack to the rope burns on his wrists.
Monk: In "Mr. Monk's 100th Case," as pictured above, photographer Douglas Thurman does this when Stottlemeyer is releasing him and removing his handcuffs after questioning him for the strangulation murders of three young women fails to turn up any solid evidence against him or a confession.
Doctor Who: The Doctor rubs his wrists after he and Robin get out of their shackles in "Robot of Sherwood".
Averted in Resident Evil 0; freed prisoner Billy, who inexplicably freed only one of his hands from a pair of cuffs when escaping custody in the intro, leaving the other dangling from his wrist for the entirety of the game, finally slips the other one off in the last cutscene and just tosses the cuffs off into the forest, leaving his wrist un-rubbed.
Cody in Street Fighter Alpha 3 has a variant, where one of his animations at the beginning of a match involves him removing one of his cuffs and shaking the hand it had been on before putting it back on.
In The Elder Scrolls V: Skyrim, if you go to third person mode right as your hands are being untied at the start of the game, you'll catch a glimpse of the Dragonborn doing this.
Sleipnir in Girl Geniusdoes this after being released from a shackle, though her wrists were covered by gloves.
Sunstone explores this extensively with its themes of BDSM; normally the characters don't do this as the restraints are intended to be comfortable and avert this; but in the instances that things go wrong; such as when Alan was separated from Ally when she was tied up we see strong red marks on her body and Alan soothing the sore wrists.
Played with too in the case of Marion and her accident; due to the fact she had her blood circulation cut off resulting in the formation of blood clots, the ropes couldn't be taken off in the first place without doing some serious damage; so we don't see Marion do this; but we do see Ally doing this to herself unconsciously as she tells the traumatic story.
Starcrossed: The Justice League rubs their wrists when they're released from shackles.
In Avatar: The Last Airbender, Iroh once uses this trope to escape. He complains to his guards that the cuffs are chafing because they're too loose. When the guard comes to tighten them, he heats up the metal, causing them to drop him.
Justice League Unlimited: "Grudge Match" Black Canary rubs her wrists after being released. It should be noted her wrists were badly burned and she had been wearing the cuffs over them. Ouch.
Truth in Television: As many police officers will confirm. Whether it is, like the Friends quote, just because they've always seen it done on TV and do it automatically, or the reassuring psychological effect of being bound and released, or just that handcuffs itch a bit, most perps will do this once the cuffs get taken off.