In Ghost in the Shell, Mokoto Kusanagi, courtesy of bionics. In the various animes,Batou was even more so, though in the original Manga he only had a few bionic parts rather than having a full prosthetic body like the Major or his anime incarnations and therefore wasn't substantially tougher than a normal human.
In InuYasha, Yokai and Hanyou can take more damage than a human can.
In Macross, Zentraedi were designed to be much tougher, physically, than a human being. Lampshaded by Breetai, who, it should be noted, had just been Thrown Out the Airlock without a spacesuit and came back in:
Shinigami life force is affected by their spiritual power. The more spiritual power they possess, the harder it is to even scratch them, let alone kill them.
Arrancar possess Hierro note spanish for Iron, a supernaturally tough skin which makes it difficult to injure or kill them.
Quincies possess Blut note Pure-blood quincies possess it from birth, mixed-blood quincies learn it with training, a method of channelling reiatsu through their body's blood vessels via reishi manipulation. By channelling this through their arteries (Blut Arterie), they can massively increase their attacking power. By channelling it through their veins (Blut Vene), they can massively increase their defensive power. Blut Vene can make it incredibly hard to injure or kill a quincy.
Shizuo Heiwajima from Durarara!! Someone once shot a ballistic knife into his chest at almost point blank range. It went in about half a centimeter.
One Piece had the CP9, an assassin group that knew the special ability Tekkai (lit. "Iron Mass"). It made their bodies as hard as iron to resist damage. The downside was that you couldn't move when in Tekkai, Jabra being the one exception as a master of Tekkai.
Rogue of the X-Men, when she was a Flying Brick (due to a certain instance of power absorption), was usually tough but not fully invulnerable. One comic had her taking a bullet to the head, which knocked her out (whereas such things would simply bounce off of other Flying Bricks).
Note that she often referred to this as "nigh-invulnerability." The "nigh" part was meant to mean that there were indeed still things that could hurt her, so it's not the Nigh-Invulnerability we speak of in trope-speak.
Wonder Woman is quite strong, and has the toughness to match as the required secondary power, but she's not so tough that she'd rather deflect bullets with her skin instead of her indestructible bracelets.
Similarly, Aquaman is able to take machine gun fire, but it does cut his skin and draw blood, so he wears Atlantean scale armour.
Derpy from the Pony POV Series is implied to have a form of this, as her special talent appears to be 'being a Determinator.' Dark World!Derpy, however, is upgraded by becoming the new Element of Loyalty, which takes this Up to Eleven to the point getting hit with lightning doesn't even seem to effect her. This seems to be a Required Secondary Power of her Super Mode, which otherwise would tear her body apart.
Not sure if King Kong or other Kaiju count or not, since relative to size, human weapons are rather puny.
The Terminator, especially in its debut film. It's not indestructible, it takes damage throughout the film. Actually getting what's left of it to stop is another story.
In Unbreakable David Dunn discovers that he has this power when he's involved in a train crash:
ER Doctor: And, to answer your question, there are two reasons why I'm looking at you like this. One because it seems in a few minutes you will officially be the only survivor of this train wreck, and two, because you didn't break one bone, you don't have a scratch on you.
Note that there are limits to his durability however. David himself believes he wouldn't be able to survive being shot point-blank, which makes for a very tense scene in the movie when his son believes he can prove his father's indestructability by doing just that.
In Robert A. Heinlein's The Star Beast Lummox shrugs off a shot from an anti-tank rifle, consumes poisons happily, and even survives an attempt at drowning. The Sheriff who wanted to kill him considers tricking him into eating explosives, but fortunately doesn't get the chance, seeing as her race might have destroyed earth if their lost princess were killed.
In the Tales of Kolmar trilogy, Varien is cut with a sword, but rather than getting his arm cut off as everyone else expected, he actually stops the sword with his arm and manages to still fight the guy. It's because he used to be a dragon, and his bones and muscles are still as strong as they were in his dragon form.
In Mistborn, allomancers who can use pewter can increase all of their body's physical abilities, which includes not only strength and speed, but also resistance to injury (and a mild Healing Factor). The drawback of this is that an allomancer who turns his or her pewter off without seeking medical attention first can simply keel over on the spot, from injuries that were trivial in their enhanced state but are much more harmful (or even fatal) to an ordinary human body. The Inquisitors, who have pewter but also a ridiculously strong Healing Factor thanks to mixing all three of the setting's magic systems, not just allomancy are considered all but unkillable.
Also, while slayers are actually a little stronger than vampires, vampires can take a more thorough beating because they're technically not alive and thus don't have to worry about things like internal organ damage.
The discipline of Fortitude in the Vampire: The Masquerade is explicitly this, giving characters a larger 'dice pool' (i.e. a larger chance) to 'soak' (reduce or ignore) damage. It also allows those who have it to partially soak damage they normally couldn't, like a vampire reducing damage from sunlight or fire. Fortitude is not an automatic reduction, however, and a bad roll of the dice means you can still get just as carved up with a knife as anyone else. There's just a lesser chance you will.
It shows up in Vampire: The Requiem as Resilience. Activating it grants a temporary increase in health levels, and allows a vampire to downgrade a certain amount of aggravated damage to lethal.
Pretty much any superhero RPG or universal system will quite naturally feature at least one way to model this.
Available in The Dresden Files RPG in various degrees of the Toughness and/or Recovery power (potentially up to all-out Physical Immunity). These are only available to characters with a suitable high concept — i.e., actual supernatural creatures, which in many games will be primarily NPCs — and must be assigned at least one "catch" that bypasses them (like the classic example of silver for werewolves).
The absurd durability of krogans is something of a running joke. Due to evolving on a Death World where they were a prey species until they invented gunpowder, they have second and often third copies of nearly every organ in their bodies (including a redundant nervous system), thick hides, a camel-like hump that stores nutrients, and great strength. As a result they can shrug off things that would kill other species, and BioWare never lets us forget it: to give you just one example from Mass Effect 2, the description of the M-98 Widow anti-materiel rifle states that it's intended for use against "armored vehicles and krogan."
It is telling that many people, including some krogan, think this about Commander Shepard. In the finale, s/he even takes a full-on shot from Harbinger's battleship-destroying main gun, and, while injured, gets up and continues. S/he's a Badass human with cybernetic enhancements, but still.
Plenty of supers at Superhero School Whateley Academy in the Whateley Universe, but Peril is a good example. He field-tested an inventor's jetpack. It exploded at two hundred feet up (so he took the blast and then the fall). He's fine now.