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Nami and Sanji have caused Amusing Injuries to Luffy more than once, even though Luffy is made of rubber, and thus isn't normally hurt by physical blows. He always seems to recover quickly enough.
Though to be fair, considering what his grandfather put him through during his childhood, their hits are probably little more than a slap on the wrist to Luffy. And they do try verbally chastising him. It never works.
Usopp gets his share of these due to how often he has a hand in Luffy's childish antics (and the fact that he's the weakest of the Straw Hats), and Chopper and Brook are sometimes in the same boat. Even Zoro and Sanji are prone to these sometimes, most often from Nami.
More in the filler than canon, Naruto often finds himself receiving bodily harm from Tsunade, Sakura, even inadvertently by Hinata one time, and the occasional anonymous female. This can be played off due to his Healing Factor but a normal person would most likely be rendered catatonic by just one of the beatings he gets from Sakura.
Taken Up to Eleven when Naruto is poisoned, and apparently would have died without the antidote, and it's played for laughs (particularly him foaming at the mouth and passing out). This is preceded by a very early scene where he gets poisoned, dramatically removes it by cutting open the wound with his kunai, and starts comically freaking out when Kakashi tells him he needs medical treatment or he'll die of blood loss.
Gai punching Lee for not listening.
Pokémon: Injuries to humans seem to yo-yo between being funny and dark depending on what the plot needed. After Ash's Charmander evolved into Charmeleon, it was a running gag for him to roast Ash'sface; similarly, there was a running gag between James and his anarchic, face-eating Victreebel (and his overly- and painfully-affectionate Cacnea and Carnivine...what is it with James and Grass-types?). However, at other times in the story, Pokémon attacks were treated as genuinely harmful and dangerous, particularly the first episode in which Ash gets chased by a group of Spearow out for blood (no, this has nothing to do with Alfred Hitchcock's "The Birds").
Also when Meowth slices peoples' faces and red lines appear. They seem to heal after a couple of seconds though.
The Team Rocket trio survives explosions powerful enough to launch them into the stratosphere at the end of almost every episode.
The main protagonist Keitaro Urashima is said to be invulnerable both in the manga and by comments from the author.
In the Christmas special OVA, he falls off the roof and sprains his ankle, putting him in crutches for the rest of the special. This is rather surprising considering he's fallen off that roof numerous times (and has had far worse done to him) without so much as a bruise before.
At one point in the manga he takes a bowling ball to the back of the head and is fine. Naru actually gets freaked out by this and demands to know if he's a zombie.
The other characters are genuinely surprised when, at the point when they're entering university, he ends up with a broken leg. Which still took a gigantic piece of masonry falling on top him like a cartoon anvil.
Averted, at least to the same degree, with other girls. When Kanako prepares to launch Kitsune into outer space, all other girls protest with a hearty, "She's not Keitaro! If you do that, she'll die!"
Very common in Fullmetal Alchemist, usually when Winry finds out that Ed has damaged his automail again. She brandishes her monkey wrench, and in the next frame Ed is lying in a bloody puddle on the ground, with Al crying in the corner and any bystanders looking horrified and frightened. The next frame, everyone is back to normal. But notable among those instances is in one episode of Brotherhood where Winry hits Ed so hard he's sitting in a pool of blood, and Al has to catch Ed's soul before it escapes his body! "I've got your soul, brother."
Note that this really only applies to Winry's wrench hitting Ed. Whenever Ed (or anyone else) is hurt in a fight, it is treated seriously and they spends at least some time in the hospital recovering. We also see notable injuries like Havoc being paralyzed from the waist down after the fight with Lust that don't heal, and prove difficult for the characters because of it.
Also applies to Armstrong following the 5th Lab incident. Ed recieved a few serious injuries in the fight against Slicer, including a cut on his forehead, a gash to his shoulder and a gash along his side. However, when Winry shows up in the hospital to repair his automail, Ed is covered head to toe in bandages. Winry asks what happened, and Ed explains that Major Armstrong, upon hearing Ed had been injured, crushed Ed in a deathly tight hug of manly affection and bishie-sparkles. Ed is shown removing the excess bandaging in the next scene, fine aside from his actual fight wounds.
Rumiya in Magical Project S gets constantly beaten up by his sister in over-the-top ways and never seems to take any permanent damage from it.
Many characters are also qualified for this tropes as Sasami(even more than Rumiya), Pixy Misa, Ryo-Ohki and Mihoshi.
The eponymous Kamen no Maid Guy is regularly beaten close to death with a nailbat as a form of amusing injury. The other characters are sometimes maimed pretty badly, too.
Bludgeoning Angel Dokuro-chan show the title character frequently pulping the male lead in very bloody and over-the-top ways that approach Happy Tree Friends levels of violence. Fortunately, she has a reset button, because she's really fond of him.
Sailor Moon: Much of the humor comes from this, with Usagi and Rei being the most frequent victims.
There's a slapstick routine involving Usagi trying to "Sailor V kick" Shingo for irritating her just after she got booted from the house for failing a test. Usagi misses and kicks the closed door, then clutches her foot in pain and melodramatically wails to be let in.
In Act 1 of both the manga and Sailor Moon Crystal, Usagi first meets her cat familiar via stepping on the cat's spine, tripping and faceplanting on the sidewalk. Luna returns the favor by maniacally scratching Usagi's face, (the marks from which disappear after a single scene) then leaping away none the worse for wear.
In episode 104 of the original anime, Usagi's feet fall asleep during a tea ceremony and Chibi-usa punches her in the foot to deliberately trigger Seiza Squirm. One word: ouch.
Usagi isn't the only senshi who was subjected to this: In "Rei and Minako's Girl School Battle", after Minako showed up at T.A. Girls Academy, and managed to piss off the teachers, she was implied to have been whipped. The beaten Minako was drawn in a comical manner, and even Rei laughed at her, upsetting her. It doesn't help that Minako was perfectly able to transform into Venus mere minutes later and defeat the Monster of the Week.
In the Sailor Moon S anime, Rei tried out a motorcycle, only to get violently flung off of it. Rei merely had a bad back and an annoyed expression to show for it (which she managed to walk off in no time). The girls just stared at Rei in confusion as they watched her get thrown off the motorcycle.
On a separate occasion, in the SuperS season, Mars had had her Flame Sniper blown back on her, leaving her with an Ash Face.
In the Makaiju arc of the anime, after getting Makoto out of a daydream, Ami was slapped on the back hard enough to send her to the ground and leave a red handprint on her clothes (though this may be an indicator that the situation was being Played for Laughs).
Excel Saga: The eponymous protagonist has been blown to bits numerous times, has fallen from tall buildings, and suffers more of such things multiple times per episode, without any lasting effects. The only exception is near the end of the anime when the Great Will of the Macrocosm is not available to do the usual Snap Back and one particular injury sticks around for a while.
Dr. Iwata is routinely beaten by his nurse sidekick in the manga, but never seems to take any lasting damage.
Pretty much everyone in the anime and even the manga is pretty close to invulnerable, really.
Full Metal Panic? Fumoffu is made of this trope. There is not one episode where Sousuke doesn't shoot someone, blow someone up, tear-gas someone, or do something that would otherwise kill said someone. However, in the first and third seasons, these things are usually very deadly.
And don't forget what Kaname does to him. In the first season of Full Metal Panic!, she hurled a concrete slab across a baseball field with enough force to hit him in the back of the head and knock him down. This trope is the only reason he got away without a broken skull or neck.
Mahou Sensei Negima! fluctuates in and out of using this, usually depending on the drama of the situation. Comically breaking a boulder over someone's head? Amusing injury. Arch-enemy impaling you with a stone spear because you happen to be in his way? You'll nearly bleed to death.
Bleach: How many times has Shinji Hirako been pummeled by Hiyori Sarugaki?
Every time someone attempts to throw himself at Rangiku Matsumoto.
Toshiro meets Rangiku for the first time.
Kenpachi "suffering" various amusing injuries at the hands of his lieutenant
Ichigo getting whacked by his dad.
Ichigo getting whacked by Rukia.
Ishida getting hit by a spirit core ball thingy.
Shiba Kuukaku beating up (mostly) Shiba Ganju or any other character that pisses her off.
Naga from the Slayers OVA's gets set on fire a lot...
L and Light's punch-ups in Death Note are oddly lacking in consequence. They slam each other in the face while playing headgames to make sure the other party's caught physically unprepared, but seem to come out a bit dirty at best. Especially odd in a series that's all about tragic/fatal consequences for very small physical actions, like writing or thinking — yet there they are, whaling on each other to no real effect.
This is largely because the arc with the punch-ups is mainly light relief from the otherwise unrelenting darkness of the plot. L and Light fight on two occasions, hitting each other three times each. They never really lose control (they argue all the way through the longer fight), and the impression given is very much that both of them are too smart to really hurt the other.
In Soul Eater, people suffer great blood loss from being whacked by books and hands. Having a scythe blade hit you on the head is one used as an amusing injury. One fight goes in the same scene from a character being stabbed through the chest, to having birds and stars around their head after being kicked.
Black*Star has been the victim of multiple bad encounters too: Groin Attacks, getting stabbed in the butt by OX using Harvar and then electrocuting him (Maka applies to this in the same episode, though indirectly), Tsubaki throwing a shrunken at him for getting caught peeping, etc.
CLANNAD: Almost the only reason for Youhei Sunohara's existence.
Played consistently sexist in City Hunter, with Ryo usually on the receiving end of some woman's wrath (most commonly Kaori, courtesy of her personal Hyperspace Mallet).
K-On: Mio constantly bonking Ritsu. That is, hitting.
In A Certain Magical Index when Touma pisses off Index she always retaliates by biting him everywhere, especially on his head. While other guys end up with lipstick marks, Touma ends up with bite marks. And pretty frequently, at that.
Similarly, Kuroko invoking the wrath of her dorm supervisor in Raligun usually ends in the Badass Normal supervisor snapping her neck so quickly she doesn't even have the chance to teleport away.
Kunisaki Izumo No Jijou: Izumo often hurls Sae against a wall, leaving a distinctive impact crater on it, whenever he tries to get too close to him.
Afganisu-tan: Usually happens towards the title character as an allusion to the decidedly less amusing stuff that happens to the real Afghanistan.
Broken ribs, injured larynx, heavy beatings from an overblown Tsundere, being dramatically sliced through by the second of the 12 Chosen Ones...ain't nothing for the likes of the Senyuu cast! Although unlike many series, the injuries stick (more or less), leading to the main character Alba complaining about his broken ribs several episodes after he initially broke them.
The anime NEEDLESS is all about this during the first half of the series. Characters get run over by motorcycles, receive stacks of bumps on their heads, one female character gets a heavy stuffed animal thrown at her head (cracking her skull), and so on and so on. But then during the second half of the series, most of the injuries are very serious, non-cartoony, and Played for Drama.
Panty & Stocking with Garterbelt is full of these, most of them happening to Chuck or Brief, although Panty and Stocking do receive quite a few Amusing Injuries as well.
Haiyore! Nyarko-san has Mahiro resort to smacking Nyarko, Cuuko, and/or Hasta when their madcap antics get out of hand. When he's really mad, he breaks out the forks. It remains Amusing Injuries in the two TV series mainly because these three are Lovecraftian evil gods and therefore can take it, and because the forks only produce the standard comedic bump; in the original light novels and the Nyaruani shorts, Nyarko starts gushing High-Pressure Blood whenever she's stabbed by one.
This happens all the time in Beelzebub. We've got Oga being beaten by Hilda and electrocuted by Beelz, the random mooks Oga pummels, the perverted Tengu Aoi has to deal with, and everything that happens to Furuichi.