In one episode of Trigun, Vash agrees to help a wealthy town mayor who is being threatened by a bandit leader...until he finds out the mayor murdered the bandit's peaceful family and took their land to build his town, at which point he stands aside when they confront each other. With the mayor's beautiful daughter pleading for her father's life, the bandit ends up shooting him in the leg instead of the killing he had originally planned on.
In Love Hina, Keitaro constantly gets Megaton Punched by the Tsundere cast (usually for something that wasn't really his fault.) There's at least two instances where the girl in question (Naru and Motoko respectively) realizes he was genuinely trying to help her, winds up for the usual violence, and then taps him on the head while he goes "huh?".
In Soul Eater, after defeating Chrona (who'd previously almost killed Soul), Maka delivers a mild version of the Maka Chop by lightly tapping him/her on the head with a book.
The Pony POV Series has this happen when the Dark World Mane Six finally confront Discord, who was mortally wounded by his sister Rancor and on his deathbed. Partially due to the mechanizations of Nightmare Paradox, the others (sans Twilight, who's realized something is wrong) deliver a No-Holds-Barred Beatdown to Discord. Apple Pie, however, merely walks up to him, gives him a "The Reason You Suck" Speech, and walks away satisfied with that.
In Killer Bean Forever, Killer Bean gets even with the bartender by going to the loo, leaving a "double flusher" in there...and only flushing once.
In the HIVE series book five, Laura is cornered by Block and Tackle. Lucy protects her by forcing the boys to stand in the middle of the hallway hugging for days. Although the rest of the cast thinks this is hilarious, Lucy worries they may starve, unable to think their way out of her mind control because they're too stupid.
In the Law & Order: UK episode "Immune", after being asked to lie in court (pretending that Jake Thorne must have misunderstood him), Casey gets even with Thorne by using his testimony to call him stupid (invoking Hanlon's Razor to explain why he was misunderstood).
In the American version, Detective Curtis insults ADA McCoy in a similar manner for similar reasons.
In Scrubs after J.D. coaxes Elliot away from her boyfriend...only to realise that he doesn't want her. After spending the whole season being mad at him, Elliot gets her revenge by giving him a note that he assumes will tell his current Love Interest (and Elliot's mentor), Dr. Molly Clock, that she's forgiven him and she doesn't need to feel guilty about sleeping with him. One mad dash later, he gives it to Clock, who reads it and says it's addressed to J.D.; "Now we're even."
The Office: Michael initially threatens Dwight with losing his job after he finds out Dwight lied about his dentist appointment, and was actually meeting with Michael's superior Jan to try to convince her to give him the regional manager position. He forgives him after Dwight breaks down into pleas for mercy, and the two even watch a movie together, but he still punishes him by having him stand on a box the next day wearing a sign that says "Liar". He also has him do his laundry for a year.
In Power Rangers S.P.D.Commander Cruger has defeated Emperor Gruumm, the one who destroyed his homeworld and left him and his wife the last of their kind, as well as caused a massive amount of pain and suffering to the Earth and the universe, and has him at his mercy. Gruumm tells him to Strike Me Down with All of Your Hatred. Cruger swings...and slices off Gruumm's horn (Cruger cut off the other one a long time ago) and arrests him.
In Hawaiian Mythology, the snow-goddess Poliahu takes revenge on her fiance Aiwohikupua after he stood her up at their wedding because he wasn't quite over his ex yet. She afflicts his other lover Hina actually a form of Pele; this is a major reason these goddesses don't get along with chills. The kahuna take Hina down the mountain to a sunny spot to warm her up, at which point Poliahu switches Hina's chills to fever. Aiwohikupua decides he'd better go talk to Poliahu, and while he's on the mountain, he too is afflicted with chills and then fever. He begs the angry goddess for mercy, and she shakes her head at him and goes back up to the summit of Mauna Kea by herself. Hina decides it's too dangerous to continue the relationship and breaks up with Aiwohikupua, who himself becomes Persona Non Grata because of his dishonesty.
In Two Gentlemen of Verona, Valentine catches his best-friend-turned-villain Proteus trying to rape his girlfriend. He decides that Proteus' punishment will be nothing more than the embarrassment of hearing the story of his crimes related to his friends and to the Duke.
In Dan and Mab's Furry Adventures , Jyrass is marked for Fey vengeance. Dan recounts his own experience: Creatures leave you alone, terrified of what the Fey in question will do to them if they interfere. The vengeance imposed upon Dan? All of his feathers fall out if he eats shellfish. What eventually happens to Jyrass? He's made Bachelor of the Year. He hates the publicity. The reason the Fey do this is because as they are virtually immortal (time is stated not to matter to them and they tend to live for very long time), they tend to take a long time to make up their minds about what the punishment shall be and they hate finding out that someone else killed off their target in the meantime.
Vinnie, a recurring character in Gargoyles, repeatedly suffers misfortune at the Gargoyles hands and finally seems to break under the pressure, muttering constantly that he's going to take his revenge. He has a huge custom gun made, which he names "Mr. Carter" and tracks down Goliath and threatens him with it. However, Mr. Carter fires... cream pies. After the pie in the face, Vinnie walks off humming, apparently satisfied with his revenge.
It should be noted that the futility of revenge is a recurring theme in Gargoyles. Several villains are hamstrung by their inability to let go of old grudges, and more than a few episodes have explicitly used this as an aesop. Vinnie is the only character in the series who sought revenge and got away with it, mostly because he decided to show mercy.
In Dan Vs. the Wolfman, Dan hunts down the eponymous wolfman responsible for scratching his car. When Dan finally finds him, his retribution consists entirely of keying the wolfman's car - and Dan is appalled that Chris would suggest he actually kill the wolfman for being a dangerous threat to society. For the sake of context, note that Dan once destroyed Canada because he slipped on some maple syrup. Disproportionate Retribution is practically the man's middle name.
On The Simpsons, after Abe and Mr. Burns are the only ones left in a Tontine agreement for a bunch of stolen paintings, Mr. Burns makes attempts on Abe's life, and even brings Bart into it. Abe has the chance to kill Mr. Burns, but chooses not to, on the grounds that it would be cowardly. Instead, he uses the fact that he held a higher military rank than Mr. Burns to have him dishonorably discharged.
One episode of the Kablam short Sniz and Fondue sees Sniz, carrying some modeling clay home, accidentally ram into a mysterious Gypsy woman. He apologizes a moment before the woman yells that she'll curse him. Since Sniz already said he was sorry, she decides to go easy on him and "only" curse the clay. Unbelieving, he shapes it into a sculpture of his brother...
In cultures where one was required by honour to duel someone who offended you, it was fairly common to "delope" — deliberately miss your shot, thus fulfilling the terms of the duel while making it obvious to all involved that you never intended to hurt your opponent, and giving them the choice of either doing likewise, or shooting you and ruining their own reputation.
Likewise, sword duels were often restrained to literal "first blood" — giving your opponent a nick on the cheek or arm, and a cool scar, rather than a serious injury (that's before they devolved even more to the point when giving each other cool scars became the entire point and the whole "fighting" thing was forgotten about).