In The Order of the Stick: Start Of Darkness, it's revealed that the Goblins' god, The Dark One, is actually an ascended goblin who was called that because of the color of his skin. He was actually a leader and a peacemaker before being killed by evil human, elven and halfling nobles during a diplomatic meeting. (Actually, sadly the nobles probably weren't "evil" per the D&D alignment system as defined by their own gods, since they "merely" did away with a goblin, not a member of the "privileged" races. But since D&D designers like to pretend that in D&D cosmology Good and Evil are Objective moral forces, having someone assassinated during a peace talk should rank as an evil act.)
Another example of how Dark Is Not Evil is the aptly titled Monster in the Dark, an extremely powerful creature owned by Xykon who hides in constant darkness as a trumpcard for him to use. However the Monster itself is a simple-minded being with childish tendencies, only acting evil when directly told to by Xykon and even then doing so ineffectively (it doesn't care to eat children, throwing them into the trashcan instead). O-Chul, a paladin being kept prisoner by the villains, recognizes the creature as not evil and befriends it within a span of three months. And vice versa. The monster ends up saving O-Chul's and V's lives from Xykon — and quite anxiously worried that its teleporting them away might have put O-Chul somewhere else dangerous.
Another strip has Belkar invoke this trope with regard to Vaarsuvius and an Evil Costume Switch, telling Haley that she shouldn't judge the elf just because of the newly added glowing eyes, wild hair, pale skin, vampiric fangs and ominous voices. Of course, V has just made a Deal with the Devil and killed an entire lineage of black dragons, so...
Even without the black dragon massacre, the trope is subverted anyway when Belkar congratulates V on entering "the deep end of the alignment pool." He was just messing with Haley.
Parodied with Tsukiko, the necrophiliacPerky Female Minion of Xykon. She thinks that because death is the antithesis of life and the Living are Jerkasses who are "prejudiced" against her for her "Beliefs", the undead are therefore kind and caring creatures misunderstood by others and that Xykon will eventually grow to love her. The Monster in the Dark tries to tell her that it doesn't work that way.
The Guides from Gunnerkrigg Court are dark, frightening (at least one of them looks downright Lovecraftian), grim, and an obvious and infallible omen of death, but if you start chatting with them, you'll find out they are nice. Unless you are a medium, by the time you can chat with them it's too late to tell the tale...
There's also Zimmy. She looks like a Stringy-Haired Ghost Girl, and acts like an obnoxious jerk to almost everyone. What's more, she has uncontrollable reality warping powers that create a hellish city populated by faceless monsters. Despite all this, she's not explicitly a bad person, wanting to be left alone more than anything.
This is pretty much the entire point of Goblins: Life Through Their Eyes.
In Shadowgirls, not only do the protagonists have some kind of darkness-based powers, but the recently revealed, rather joyfully sadistic protagonist has light-based powers.
In Erfworld, Vinny Doombats has the appearance and bat-themed trappings of a classic Dracula-style vampire. He's also the loyal right-hand man to the color-coded "good" side leader, and acts on straightforward "good" motivations (friendship to the aforementioned leader and recognition that the enemy is a dangerous aggressor).
While Vinny is unambiguously good, the leader of his side is portrayed as morally ambiguous, and his fervent religious and feudalistic beliefs (which keep him in power) and overall motivations are quite unsympathetic.
But not as unsympathetic as Lord Stanley, the leader of the opposing side, who is a mean, cowardly and selfish guy with a Napoleon Complex who threatens to "disband" (read: execute) members of his own troops if he feel slighted.
And by now, even Stanley shows some more sympathetic qualities, showing some remorse for the effect linking his Eyemancers (and then breaking that link) had on the Foolamancer Jack, acting as an inspiration to his men when they are surrounded by Transylvito forces, and thanking Jack for saving his forces, as well as showing doubt as to whether he is doing the Titan's will, suggesting he genuinely believes himself to be a tool of the Titans' will.
Really, Don King's "fervent religious and feudalistic beliefs" are a reaction to the political climate and a desire to remain closer to sides like Jetstone (not to mention a healthy hatred of Stanley). Before the battle for Gobwin Knob, he took a much more pragmatic approach to governance with the creed of the "best person for the job", even going so far as to name a non-Royal Heir Designate. The Values Dissonance between the old Transylvito and the new Royal Crown Coalition is a minor plot point, and a cause for unease in characters like Vinny and Caesar.
The Watcher of Mort (God of Death) in Exterminatus Now look like empty tattered floating black robes with streams of ash running out of the openings. However, their holy mission is to protect hallowed grounds and the corpses resting therein from graverobbers and occult defilement. They hate necromancers who turn corpses into zombies. But they caution any passing "hero" not to harm the poor zombies further, as they are mere "victims, innocent puppets", who must be returned to their rightful resting places.
Last Res0rt and the Dead Inside. Filled with Vampires, Zombies, and Djinn, they certainly look set up to be evil, complete with "Dead Eyes"... except Jigsaw's shaping up to be a Friendly Neighborhood Vampire, and if anybody's come across as evil right now, it's the angel-winged Celeste.
Planes Of Eldlor has a dark elf who is far more apathetic than evil. Also, the sinister-looking riftwalker dragons, which are all black with glowing violet eyes and blood, but do not appear to be evil.
Digger befriends a strange creature she calls Shadowchild who turns out to be a feral demon who can eat your shadow, sending you into a fatal coma. Shadowchild is also the most innocent and well-meaning character in the comic.
Rilian the necromancer in Dominic Deegan masquerades as a jolly guy called Brian in the Around the World arc. After he reveals his true identity, one of his associates remarks that he was not deceiving Dominic: The masquerade was a rare opportunity to let loose and be himself for a change. The personality, the philosophy and even the body was all him, the only fake thing was the name, and even that was just the modern equivalent of his real name.
Silent Hill's Alessa Gillespie is either Chaotic Good or Chaotic Neutral, depending on whether you assume that her motivations are to prevent the birth of some sort of demon goddess and protect the world, or just to end her own suffering, but either way, she is absolutely freaking terrifying and she is preventing the end of the world.
Homestuck: Trolls may be a race of horned, yellow-eyed, fangedJerk Asses with a tyrannical society built on massiveValues Dissonance, in addition to being actual internet trolls, but most of them aren't really so bad once you get to know them better. In general this trope and Light Is Not Good apply to their culture, which has a view of of the moral status of light and darkness inverse to that of mankind as a result of their nocturnality and the dangers of exposure to the Alternian sun, making it most fitting that in recent events almost all of the biggest threats facing the trolls involve bright light.
It also seems the black-carapaced Dersites are not all as evil as their queen; WV, before his exile, united Dersites (black) and Prospitians (white) against the tyrannic monarchs of his kingdom, and both he and fellow Dersite AR are varying degrees of Lawful Good.
An important event early in 2011 involved a battle between a hero of Hope and a hero of Doom. The hero of Hope was a genocidal maniac and the hero of Doom was a good guy, albeit an occasionally moody one.
Liz from Blip is a vampire, wears black all the time, has short, blue hair, drinks blood (animal, not human), and is really nice once you get to know her. Sure, she used to be evil, but not anymore.
In Achewood, when Philippe falls asleep in the garbage dump where he went to find a missing couch, he's carried off by two horrifically disfigured men. They are later revealed to be Zell and Cory, two drifters who got their disfigurements in a flophouse fire, and were just taking him to their home so he'd have a safe place to stay.
Played with in Slightly Damned. The Demons do have some evil tendencies, but are neither necessarily nor wholly evil - the most prominent Demon in the series is Buwaro, who is an absolute sweetheart, and even Lazuli, who is definitely evil, seems to have genuinely cared about her partner and is pursuing the heroes partly out of revenge for his death.
Tales of the Questor features a suit of pitch-black armor with red glowing eyes in the faceplate, enspelled to move by itself and haunted by the ghost of the knight who died wearing it. Said ghost turns out to be a courageous Knight in Shining Armor (paint job notwithstanding), and without him shaming the armor's current wearer into returning to the fray, Quentyn would almost certainly have been killed by the red dragon.
Curio from morphE is a Moros mage who controls shadows and the ability to perform "Death" magic. He is a 15 year old timid wallflower and in no way represents the traits of his abilities.