Though Dungeons & Dragons tends to be pretty bad for "dark equals evil", this is not always the case. Even necromancy isn't always evil; while most of the necromancy-themed prestige classes don't allow you to be good, they don't require you to be evil, and a wizard specializing in necromancy may be of any alignment. Basically, in most settings there used to be three main types of people who chose Necromancy knowing what they want: some came there to create undead and drain life, some for healing/resurrecting, and some to ward off and destroy undead. Old Complete Necromancers put raising mindless undead as such in "gray" subdivision (while unappetizing, it's just walking remnants), anti-undead and defencive spells in "white".
A subversion existed in the older spell-casting rules: Healing spells were in the Necromancy school, until they were moved to Conjuration in the Third Edition. However, there are still some beneficial Necromancy spells, such as False Life.
By 3.5 core rules, very few Necromancy spells are evil. The Evil Necromacy spells are any that create undead creatures, causing disease via Contagion, making unholy water (the opposite of holy water, natch) via Curse Water, the life-draining Death Knell, the torturous Symbol of Pain, and the "Evil Eye" Eyebite. Oddly Deathwatch is described as Evil even though the only effect of the spell is to know how close nearby creatures are to dying. Strangely, not even instant-kill spells like Finger of Death are given the "Evil" stamp by the game - and most of the Evil spells are available to priestly Clerics.
Presumably due to the flavor text mentioning the caster "using the foul sight granted by the powers of unlife", but that's merely that... flavor text. And not that neutrals were utterly prohibited to have anything in common with undead. It's only a "detect hit points" spell, for God's sake. Giving it an evil descriptor is ridiculous. Especially since the 3.5 edition Spell Compendium contains a spell that basically does the same thing: It allows player character clerics to closely monitor the hit points of their allies during combat, how wounded they are, etc., so the cleric will instantly know when and where to dispense healing.
Arguably, the "crunch" that is backing that flavor text IS the fact that it has the Evil descriptor, thus signifying that casting the spell is an inherently evil and alignment-altering event even in the absence of any other visible moral aspects.
What's really odd, is that Deathwatch is on the spell list of the Miniatures Handbook Healer, which is required to be Good, and Book of Exalted Deeds Slayer of Domial, that loses all powers if it commits an evil act. Hmm.
Clerics are much much much more affected by alignment descriptors than Wizards; indeed, only with something like the Spell Focus (Evil) feat do alignment descriptors have any game effect on arcane spellcasters. Clerics, however, can't cast spells opposed by their alignment. The goddess Sharess from the Forgotten Realms might be partially an instance of this - not a dark goddess, but she certainly brushed with Evil is Sexy when confronted by Shar before ultimately ending up good. Someone check my references though...
The "Book Of Vile Darkness" describes evil, and what has to be done for it to be evil. Spells like "Finger Of Death" are not evil— Killing something is a neutral effect, the reason why is what's morally affected. However, spells that cause unneeded pain or torment, like "Wither Limb", which causes the target's limbs to shrivel terribly, are evil simply because you could incapacitate an enemy in a much less cruel way. Otherwise, in a game like D&D, where a Paladin loses all abilities for doing any evil, even just attacking would be evil because it's causing harm. It's okay, because it's not torture.
In Lords Of Madness, a book about Abberations,there is a race called the Silthilar, creatures that were once elven wizards but turned into hive minded swarms that coalesce into what can only be called a Starfish Alien and specialize in grafting strange and bizzarre parts onto humanoids. And they are Chaotic Good.
4E has an embodiment of the trope as a basic character class, the theurgy-inclined Warlock. The three paths they have to their particular brand of Pact Magic are, as follows: Making a literal Deal with the Devil for more offensive Black Magic, consorting with The Fair Folk for Psychic Powers and various trickery, or making a contract with an abomination for a mix... and they are quite as capable of being good as any other core class, although the book mentions they have great capacity for evil as well, but that's the same for all other classes. There's even the Dark Pact in the Player's Guide to Faerun, in which you make deals with shadowy beings of darkness, and you are no more forced to have any alignment restrictions either (though it does promote acting like a dick in some cases).
That's because the Dark Pact has a modified version of Cast from Hit Points applied to it; some of its spells can be made more powerful by draining Hit Points from allies, while others cause a penalty to allies in exchange for working. And what about the Vestige Pact, which revolves around drawing upon the spiritual remnants of powerful forces and entities that displayed either great authority or awful capabilities in life? Or The Sorceror King pact from Dark Sun, based around getting power from the horrible wizards who get their powers from draining the lifeforce of the planet?
Of course, don't forget the fact that 4E is one of the few editions where Undead are not Always Chaotic Evil. In fact, in the upcoming Heroes of shadow, they have a Necromancer wizard build.
The 'tiefling' player character race are descendants of fiends and mortals and look accordingly. While their looks and history give them a definite push into the dark and brooding loner direction, any given tiefling may still be of any alignment.
Though since their appearance back in the early editions of the games, tieflings have been described as being 'mostly evil.' Planescape stated about 90% of tieflings are, in fact, evilly aligned. Which leads to a curious disparity; apparently being demon-blooded makes you less likely to be evil than just being born into certain completely natural, mortal races.
And the most famous tiefling is Rhys. Not only true neutral, but the head of the Transcendent Order, who tend to balance things around themselves involuntarily.
Planescape also has jabs at Clueless such as "they think everything with horns is Eeevil".
Sigil also has a number of factions that fit the trope:
The Dustmen faction are basically all creepy goths who hang around with the undead, but their faction philosophy is akin to Buddhism and they're responsible for Sigil's funerals, proper treatment of the dead and counselling those left behind. The undead they hang out with volunteered to have their bodies reanimated.
The Doomguard, who believe in entropy and the inevitability of everything that exists eventually crmbling to dust with nothing remaining at the end of time. Some extremists believe that they should speed up the process as much as possible, while others support the constructions of new buildings, because it includes chipping away mountains and cutting hundreds of trees, and the new building will only last for a few hundred years if it doesn't burn down much earlier.
The Bleak Cabal are extreme nihilists, most of whom have at least a trace of mental illness. But despite that and their ominous moniker, they run Sigil's orphanage and soup kitchens, as well as asylums that at least try to not be Bedlam House. If there's no point to anything, there's no reason not to help each other, nor is there a reason to make the Crapsack World worse.
The sharakim in D&D 3.5 are a race of orclike humanoids who are mostly kind and goodhearted. Likewise, the mongrelfolk, who go back to 1st edition, are deformed mish-mash hybrids that look like man-eating monsters for the most part, but they really just want to be left alone.
Another 'not evil' race from D&D, possibly from Mystara, were the Diaboli, who basically look like an entire race of wingless Big Purple Devils — cloven-hooved goat-like legs, small nubby goat-like horns, forked tongues, bald or hairy or in-between, long tails with curved toxic stingers on the end. The twist? They're peaceful people from the Plane of Dreams who are exiles after evil beings (Nightmare Spirits) took over their dimension, and the reason they seem to be so secretive and isolationist is that they find US disturbing and demonic to behold. Even their stingers only inject sleeping venom, and their racial alignment is Usually Chaotic Good (the vast majority of those who aren't are Chaotic Neutral or Neutral Good, with Chaotic Evil being a very rare occurrence).
Speaking of races, drow serving Eilistraee (Chaotic Good goddess) managed to implement bothDark Is Not Evil and Good Is Not Nice: they are supposed to be more benevolent than one would expect from an average surface elf, let alone drow, but frequently are too paranoid, aggressive and/or even Holier Than Thou to be a good company.
Also Saulofein in Baldur's Gate II. Throughout the quest he is involved in, he is extremely rude to you, takes every opportunity to insult you, he is sarcastic and seemingly just as heartless and cruel as all the other drow in the city. At the end of the quest you are supposed to deliver a silver dragon egg to the matriarch, who will use it to gain favour with a greater demon she will summon. You yourself are on a quest to actually save the dragon egg. You are provided with an opportunity to do so when the Matriarch's daughter gives you a fake egg, which will anger the demon, who will kill her mother, after which she can then offer the real egg. But just before you can go on, Saulofein will show up, and reveal that he has been spying on you, and if you have secretly performed good deeds before, he will have noticed. But instead of attacking you, he reveals that he is actually secretly a worshipper of Eilistrae, and his whole rude, insulting, sarcastic character was just a ruse. He then gives you a second fake egg which you can switch with the real egg. When both the Matriarch and her daughter offer their eggs to the Greater Demon in turn, hilarity ensues.
The Al-Qadim campaign setting went out of its way to embrace this trope, such that goblins, orcs, ogres, and other races that are just there for the heroes to kill in other settings were actually peaceful, productive members of society; the only races that were Always Chaotic Evil were explicitly supernatural, like the yuan-ti, yak-folk, and noble efreet. Likewise, the Eberron setting played goblinoids as aggressive but not inherently evil, while the orcs were actually responsible for protecting the world from monsters. And, of course, the draconians in Dragonlance were created to be the vile servants of the Gods of Evil, but once the gods went away, a lot of draconians realized that not being willing tools of evil has its ups.
While usually the good creatures get short shrift in the Monster Manuals of all the editions to make space for yet another thing the heroes can fight, there are a few which play this trope straight. Most notable might be the Asuras, good-aligned celestial beings with flaming wings who embody a holy fury. Though virtuous, the average asuras makes a mortal Knight Templar seem more like a Gentle Giant.
Well, mythologically speaking there really are three kinds of undead, which in D&D terms could probably be called Good, Neutral and Evil : for Good we have those folks which subvert the natural order (born-lived-died-end) in order to help others, such as the bhoddisattva of Buddhist lore, i.e. guys who have earned their way out of the whole reincarnation chore and into Nirvana, but stay down here to help others on that path. Which is pretty cool of them. For Neutral, we have the "unfinished business" kind, those undead who, in life, were focused on one goal so hard even death ain't an obstacle. Mankind's wishful thinking, there, OK, but in any case, the task in question can be Good ("protect my baby heir"), Neutral ("finish my research") or Evil ("Kill my murderer in gruesome ways"). And then we have the Stupid Evil, "RRrrrGrowl, Braiiiiins" kind of undead, which aren't nearly as interesting.
Old Lords of Darkness mentioned things like skeletons marching out of crypts to save their descendants. Forgotten Realms officially had at least two undead paladins — didn't consider the grave important enough to stand between them and the duty and all that.
Also, one has to note that, in 4th Edition thanks to the little appendix at the end of the Monster Manual, it is actually easier than ever to play as a good version of a normally evil race and have it actually be playable crunch-wise.
Very few non-Outsiders are Always [Something] Evil, meaning your average mortal race known for its evil is quite likely to have less than 90% of the population be evil. This was showcased by things like the Orc minority in Thesk in the Forgotten Realms, most of which were Lawful Neutralnote Orcs were usually Lawful Evil in Second Edition, when those Orcs settled down in Thesk.
The Scarred Lands setting has a location known as Hollowfaust, aka "the City of Necromancers"... which defies every stereotyped expectation of such a city. Normally the only undead seen are mindless skeletal undead (animated skeletons and bone golems), because zombies are seen as both too disturbing and too unhygenic, the populace are some of the wealthiest, healthiest and all-around best off in the setting, and there are strict laws against the abuse of the populace — necromancers who seek undeath are actively discouraged from joining The Magocracy that rules the city, and only the worst criminals are allowed to be used as "test subjects".
The gods and demigods that make up The Dark in Nobilis are harder to characterise as Not Evil than their opposite number are as not Good, since they believe above all else in inducing humans to suicide. Their work generally involves systematically destroying everything a given person cares about. However, they have some redeeming features: They are arguably a fundamental and necessary part of human nature, having sprung from the fruit of the Garden of Eden. They will almost never kill, since a murder is a suicide prevented, and may even step in to avert needless death. The more someone resists their tortures, the more likely they are to simply leave them alone for an easier target, effectively purifying the gene pool. Some believe that the point of their work is to make those they test stronger. However, as the book points out, cruelty for kindness' sake can be much more thorough than the other kind...
They've gotten a bit nicer in 3E: While the Dark still wants to drive humans to their own deaths, they want humans to also have the freedom to choose it. Thus, life under the Dark may be short, but it's a lot of fun.
In Warhammer 40,000 the Black Templars and Dark Angels Space Marine Chapters are... no more evil than their peers, although the Dark Angels are one of the shadier Chapters of Space Marines, more concerned with personal redemption than serving the Imperium itself. Though, the Dark Eldar are definitely a lot worse than the Craftworld Eldar.
The Black Templars are even more fanatical than usual and the Dark Angels...well. It's also not fair to label all the Space Marine Chapters as "evil" - the Ultramarines and the Imperial Fists are examples of a couple of the more genuinely heroic chapters. The Raven Guard are a better example of Dark Is Not Evil.
The Soul Drinkers are a dead-straight example: their name sounds pretty nasty by itself, their motto is "Cold and fast", and as a pleasant bonus the vast majority of them are mutated in some way, with their Chapter Master having the legs of a giant spider. They're the closest 40K gets to Neutral Good, fighting both the destructive madness of Chaos and the tyranny of the Imperium.
Then there's the Space Wolves, who all look like large, wolf-fanged, viking Space Marines, who are all pretty damn pissed that the administratum decided to wipe out the remaining survivors on a planet they had just saved. Needless to say, they are probably the least tolerating towards the administratum's actions of all the chapters still in the Imperium.
The Salamanders have jet-black skin and glowing red eyes, but are actually concerned with protecting innocent people instead of just slaughtering the bad guys (and whoever gets in the way).
In the novel Eisenhorn, the eponymous Inquisitor is surprised that a Librarian of the Deathwatch Chapter is a very erudite, even nice, guy, despite being a veteran xeno-fighter with Terminator honours.
In Brothers of the Snake, the distinction can be drawn between two of the senior marines. On one hand: Librarian Petrok, a walking CMOA and superhuman killing machine whose attitude towards those around him, particularly Priad, could nevertheless be described as 'chummy'. He is given to occasional whimsy, and likes to "remind himself that he has a soul". On the flipside of this, there's Hero-Captain Phobor, a more conventional Astartes in that he's a humourless, unrelenting psychopath who is 100% devoted to warfare and nothing else, and is contemptuous of weakness to the point of sentencing the officer corps of an Imperial Guard regiment to penal legions for failing to win a battle of attrition.
The ones in black armor and face-concealing skull-painted helms? Those are Space MarineChaplains, whose job it is to maintain their brother's faith through exemplary leadership.
Speaking of bone, the harlequin death jesters wear black, a skull mask, and bone-studded armor, and fight with a minigun shooting envenomed "shuriken". The harlequin are sworn foes of the Ruinous powers and will occasionally appear seemingly out of nowhere to aid those fighting Chaos.
While they are hardly particularly good (to other races, they tend to do well enough by their own) the Black Guardians of Ulthwe are veteran foes of chaos and were allied with the Imperium during the latest Black Crusade.
In Mage: The Ascension there were the Euthanatos mages, who were down with death and decay, were resident experts on where the souls of the dead go, and were dedicated to making sure all things die at their appointed time. Despite all that they were still supposed to be good(ish) guys, and firmly disapproved of things dying before their appointed time.
Vampire: The Masquerade had the Nosferatu (who were all hideously disfigured) and Gangrel (who start normal but become more and more bestial-looking over time) vampire clans. Despite being full of monstrous-looking freaks, neither of them were "baddy" clans... Well, not any more than the other Camarilla clans, anyway. Still blood-sucking undead monsters, though.
Kindred of the East introduced 'vampires' who were more like Asian hungry ghosts than anything else, feeding off of chi energy. One group had a karmic imbalance towards virtue and duty, and were driven by those emotions. They're still undead, soul-siphoning abominations who use powers which range from rather creepy to outright squicktastic, but their souls and powers still feed off their sense of righteousness and obligation. Even the Devil Tigers were portrayed to usually be doing some sort of 'good' by visiting their vast cruelties and depravities on people who need to suffer such things.
Changeling: The Lost has the Darkling seeming. They explicitly had some of the "light" (however you want to define it, it might change from person to person) taken from them in Arcadia, leaving them rather warped and with an aversion to sunlight. One of the kiths sees ghosts; another drains life from passerby. Their major Contract gives them power over darkness and shadows... and nothing stops them from being decent people.
The Moros Path of mages in Mage: The Awakening have Death and Matter as their ruling Arcana. Their powers are thus heavily rooted in destruction and decay. For the most part, however, they're not evil, just depressing; you'd be the same way if you saw the world through the eyes of the dead, too. (This is slightly mitigated by the fact that they just beat out the other Paths for Left-Handed Legacies, with three Moros-specific.)
Vampire: The Requiem had the Septemi, a Daeva bloodline whose bloodline weakness is that its members find it hard (losing a Willpower point) to not to "indulge" in their virtues whenever the chance happens. What makes it funnier is that the Daeva clan weakness is that they lose their Willpower point everytime they do not indulge in their vices when the chance happens.
Geist: The Sin-Eaters revolves entirely around characters who die, make deals with death-spirits, come back, and sling necromancy around like it's nobody's business. These guys deal with the dead more often then virtually every other game, and most of them use their powers to help cross the dead over. Of course, some go insane and others become grim reapers.
The Nightbane RPG from Palladium books is about characters who are gifted with incredible superpowers that they use to fight off demonic forces that secretly rule the world. Except the superpowers all relate to darkness or blood, and they have to transform into hideous freaky-deaky monsters to use their powers.
The Golgari Swarm in the Magic: The Gathering setting of Ravnica are a cult of elf and human necromancers who use zombies as labor... but they're also an indispensable part of Ravnica's society, providing food and waste disposal services. A lot of them are indeed black-hearted knaves who sacrifice unwilling people to raise them as undead, but one of the heroes of the tie-in novels is the leader of the Golgari, who's working to reform them after the death of his evil sister.
What about Black? Its iconic creatures are zombies, vampires, and demons. But they aren't defined as strictly evil, only greedy or ambitious. In theory anyway. In practice it's also heavily associated with sadism, desecration and murder.
However, Kamigawa's main protagonist, Toshiro Umezawa, is black, while its main antagonist (among mortals, at least), Konda, is white.
Mark Rosewater discusses Black's ideology at length here.
The vampire planeswalker Sorin Markov is another black Anti-Hero. He's scheming, vicious and paranoid...but at the same time, he managed to work together with two other planeswalkers to seal the Eldrazi in their can.
In fact, given that he is singularly responsible for nothing less than the creation of at least one virtuous god-figure, purely to defend the humans of his home plane, Sorin is capable of remarkable compassion and foresight (although in this set, he is part-white, unlike before, though this might be due to his use of plains magic, as mana cost often isn't entirely accurate to the character's personality).
To a lesser extent, gargoyles. Although they are technically White, their appearence is quite◊ demonic◊
Magic has gone back and forth on this when it comes to Black. It didn't help that the ultimate Big Bad of the setting for the first several years, the Clockwork Hell of Phyrexia, was mono-Black. Obviously, the team recognized their Dark Is Evil problem of the past, because the New Phyrexia is five-color.
Avacyn from the Innistrad Pack. Seriously, look at her◊! Would you guess a gothic woman with deathly pale skin and black leather would be the guardian angel of mankind? (Of her plane, of course. She can't planeswalk)
The PAX video heavily hints that her dark look was adquired due to her stay in the Helvault with the demons. If that's the case, this defenitely this trope, as the demonic influence had no effect on her morality.
Chainer is another Black aligned protagonist (before being corrupted, anyway), as is the Sapling of Colfenor, Teysa, and, as of Innistrad, Liliana Vess (who was just an anti-heroine in her previous appearences anyways).
In the Mutants & Masterminds third party setting Halt Evil Doer!, the principle hero team features Splotch, a darkness manipulator who looks like a walking ink blot test. Not only is he one of the good guys, but he's also an Expy (or Captain Ersatz depending on your point of view) for Spider-Man.
In Exalted, Five Days Darkness sure sounds like he'd be an evil god—he's got a sinister name, a backstory as the first shadow cast by the Unconquered Sun, he was cast out of Heaven because the other deities didn't trust him, and he's a Creature of Darkness, a descriptor usually used to refer to enemies of Creation. However, not only is he one of the good guys, he's also one of the nicest and least corrupt gods you're likely to meet.
We also have Green Sun Princes, the True Infernal Exalts. Yeah, sure, they're basically demonic demigods, they have to fulfill their Urges or risk building up Torment and the way to reduce it is to act like a B-Movie supervillain...Except those Urges can easily be traditionally Solar goals (yes, Light Is Not Good and all, but Solar goals tend to be morally neutral) and the guy you are doing the villainy gig on is your choice. Word of God says the Yozi screwed themselves over on that one.
Likewise, Abyssals may hurt the world through their very existence, but some of them work to keep the ghost/mortal deals fair (although the White Walker is a bit myopic when it comes to the feelings of mortals), and some of them, such as Fallen Wolf of the Cutting Sea, would very much like to stop hurting the world now please.
Lunar Exalted are not to be overlooked here - they can make zombies with Charms natural to their Charm set, slap some rather disturbing mutations onto people, and turn into horrifying things, but their power is no more inherently harmful than that of a Solar or Sidereal.
The devils of the Righteous Dead (from the Daystar supplement) also qualify. They were once righteous mortal souls chosen by the Unconquered Sun to Ascend to a Higher Plane of Existence, but they failed to climb the whole way, becoming horrible monsters that exist to torment other righteous dead who take the path of suffering. And they are damned well going to do their job, because it's the only way to cleanse these ex-mortals of their sins and make them ready to join the Unconquered Sun's company, and in so doing, prevent them from falling into suffering as they have.
Finally, the whole field of necromancy is an excellent exemple of this trope. Sure, it is now almost only used by Abyssal exalts (who are at best anti-heros) and Deathlords (who are very much evil indeed), but it was created by the Twilight caste Solar Exalted during the First Age in order to use the energies of death for their own righteous (well, at least theoretically) goals. Granted, some necromantic spells involve really gruesome rituals, but simply being a necromancer won't make you evil, or doesn't require you to be evil in any way. (And it is useful to point that "regular", non-necromantic sorcery, does have spell to level cities, permanently turn someone into your obedient slave, or utter a curse so horrible it tears the target's soul.)
Scion has any number of gods of death or darkness among the roster. Their Scions are perfectly capable of being decent folk - one of the sample characters on the hero side is the daughter of Baron Samedi, Loa of death. Likewise, just because your patron god is generally considered evil doesn't force you to be a villain - the rules allow Scions of, say, Loki or Set to be heroic.
There's Orlanda Elliot, daughter of Xipe Totec, the Aztec death-rebirth god who is noted to be one of the most beloved to the people who worshiped him because he made spring come every year, and all things considered, probably a nicer guy than Tezcatlipoca, the father of the corresponding good Aztlani Scion.
From fan work, we have a semi-example in Po, Polynesian Titan of Night. Sounds like she would compete with Sobe-No-Kumi for the "Bastard of the Eon" award, right? Nope. Instead, she represents potential, meaning that her Genius Loci form is a beautiful forest under a clear night sky where life thrives. She's actually rather fond of life as it is now, and it's outright stated that her conquering reality wouldn't be the worst thing in the cosmos. Unfortunately, she doesn't discriminate between monsters and humans, meaning that her Earth would be a safety hazard. So, in this case, Dark Is An Anti-Villain.
In Pathfinder, one creature is a huge, ugly scavenger that many immediately assume is evil because it eats "waste" and isn't a nonsentient animal. It's often hired as a living garburator by non-humans.
The Warhammer world has a few examples, notably the followers of Mohr, god of death. His paladins dress in armour carved from obsidian, but are as heroic as anyone in thissetting. Oh, and they really hate the undead.
Speaking of Warhammer, the undead themselves sometimes qualify for this trope themselves. Blatantly obvious are the Tomb Kings, who for the most part just want to be left alone and be left to rest. The Vampire Counts, on the other hand, can range between anything from the occasional Anti-Villain to the far more common rogue, mainly because they are a far more varied bunch than the Tomb Kings.
There are also the Dark World Fiends, which are an odd case. They were villains in the anime, where they were clearly evil, but the flavor text of Zure, Kight of Dark World and Renge, Gatekeeper of Darkworld portrays them as renown heroes, while the Master Guide 2 support book claims that they aren't evil at all. Obviously this was a case of Adaptational Villainy on the anime's part.
The reason the Ghostrick entered the Yu-Gi-Oh fray was because fewer people believed in them and they were lonely, and they seem to be more interested in scaring people than fighting. Their tactics of bypassing their opponent's monsters using their Field Spell supports this.