Beyond the Western Deep is by its own creators admission meant to be a morally gray piece, opposing the veryBlack and White Morality of the Redwall series it was inspired by. None of it's Funny Animal races are inherently good or evil, and the main conflict of the series is too complex to be categorised as justified or not: one of the races, the Ermehn (which are anthropomorphic weasels, strongly averting the usual Wicked Weasel archetype with many sympathetic characters and an Anti-Villain for an antagonist) have been banished from their homelands to die off in the wastes, and the series is focused on the rising tensions across the world as they want to remain alive by reclaiming said territories.
Last Res0rt, with several condemned criminals in its ranks, usually sits firmly here; while most of the characters involved are criminals (and even some of the volunteers are only a couple notches above 'em), it's only when Arikos, Geisha, or the Celeste get involved that the comic slips into Black and Gray Morality.
Angels 2200 does not go into the causes behind the colonies' revolt against earth, and both sides are composed of leaders who use morally dubious tactics in order to win and soldiers who only want to stay alive. Then again, depending on what the true origin of the genetic plague is, one of the sides might count as black.
Word of God claims that this is the case in Drowtales, where the story is shown through several viewpoint characters, neither being portrayed as good/evil and with fairly realistic motivations for their actions. It also features a character who in most stories would be a shoe in for The Hero who is a horrifically abusive parent, while her counterpart on the "bad" side is unquestionably one of the best parents in the series. And even the character who so far seems to be clearest example of the Big Bad sill remains somewhat sympathetic and has a point on some issues.
In the very Not Safe for Work webcomic Felarya, man - eating monsters are depicted as no worse than the humans they eat.
The conflict between Agatha and Klaus in Girl Genius. Klaus has every reason to want to keep Agatha locked up until she's proven trustworthy, and (given recent events) can make a pretty good case for killing her with fire. On the other hand, Agatha really hasn't done much to deserve that (yet), aside from getting the Big Bad stuck in her head, and she's got every right to fight back (particularly when her friends get caught in the crossfire). Not forgetting Othar, who is killing off sparks. He's deluded, but considering somespark'screations he's kinda right.
Othar slips out of grey if you read the side materials in his point of view: his solution to the problems caused by Sparks is to kill them all. He's pretty OK with a train going into a canyon with everybody aboard when he finds out they're all Sparks. Let's hope he never realizes the definite possibility that he will have to kill all humans to permanently eliminate Sparks.
Klaus' reign over Europa itself. At first, it's pretty much implied to be an Evil Empire, with Klaus at its head as the Big Bad and his son as the main love interest for the protagonist. Then you read about his backstory and what Europa was like before Klaus: note There were several years in which Klaus and the heroic Heterodyne Boys roamed Europa as adventurers. Before the Boys, the Heterodynes were actually very brutal, very sadistic mad scientists with no regard for human life and a massive army of fiercely loyal superhumans at their disposal. The idyllic times of the Boys ended when one of their wives, who was cheating on her husband with Klaus, drugged the latter after a tryst and presumably abandoned him in a place he would be hard-pressed to ever return from. Then she engineered a series of events that led to the disappearance of the Boys, the orphaning of her daughter, and the total destruction of peace around all Europa, earning her the nickname The Other. By the time of Klaus' return, he has almost no choice but to engage in the most brutal methods possible in order to make the region livable again, including usurping power from every noble imaginable by taking their heirs as hostages. It takes this and an internal betrayal within The Other's faction in order to bring Europa some stability. When The Other's return nearly two decades later sets off a chain of events resulting in both Klaus and Agatha being put out of commission for a while, Europa degrades right back to chaos, and that's with most of the rebelling factions banding together to support the new Baron - showing just how necessary the previous Baron's ruthlessness really was.
The main conflict in Juathuur is between control and freedom. Both sides have their reasons, and their differences are mainly due to age gaps (as the 'control' side grew up in a world torn by war, and the 'freedom' side did not). See the comic page for details.
The main characters of Narbonic are a mad scientist, her henchwoman who loves to destroy things, her henchman with a deep dark secret not even he knows, and a superintelligent gerbil whose efforts to do good often cause more havoc and chaos than some of the evil plans afoot.
The Kingfisher: Both Theodore and his sworn enemies - the vampire progenitors - are uncanny, manipulative, and monstrous. It's telling that the protagonist has not committed to a side.
Lackadaisy is full of this. Even the Spoiled Sweet, pretty girl who mainly works the restaurant front knows how to use a gun, is still a pretty big part in the operation, and in a recent arc, is still responsible for a large shipment of booze going to Lackadaisy. Basically, nobody in the comic is blameless, and it reaches truly ridiculous heights in the more recent arcs.
In Off-White, the dark wolf spirit Hati is trying to save the world, but he's willing to kill (or at least threaten to kill) Sköll/Ike's innocent pack mates to do so. Meanwhile, the white wolf spirit Sköll wants the world to die, but the world is going to get rotten anyway because the guardian of good died so goodness is dying with her.
The Forever War between Angels and Demons in Slightly Damned. Neither species is inherently good or evil, and both have committed atrocities, as you might expect in a war that long.
In Terra the Forever War between the United Earth Coalition and Asurian Empire is a fairly dark version. Both sides are responsible for atrocities, and both sides also have good people who are just Punch Clock Villains (one of the main characters joined the UEC military to feed his family, not out of ideology). The Resistance is A Lighter Shade of Grey: they're fighting for their homes and loved ones and have the goal of forcing both sides to the negotiating table with the hopes of ending the war and setting up a Fictional United Nations, but they use assassination as a primary tactic.
Erfworld is centered around the conflict between Gobwin Knob and the Royal Crown Coalition led by Jetstone. Gobwin Knob is led by Stanley who is convinced he is following the will of the Titans and many of his subordinates are merely trying to survive against their enemies. The members of the RCC have good reason to try to put down Stanley, as he's been attacking most of them in his quest to get the Arkentools. Jetstone, however, doesn't really have a reason to hate Stanley beyond the fact that he isn't a Royal, which they believe to be the only proper rulers in Erfworld. Even so, they still value honor and justice in battle, which Stanley and his Chief Warlord Parson don't. The whole thing is further muddied by the very nature of Erfworld, where open warfare against someone is virtually the only way to survive, much less grow, and the local laws of physics promote a forever war.
Draconia Chronicles: Originally, the central conflict had the Tigers as the clear good guys and the Dragons as the clear bad guys. However, with the addition of some sympathetic Dragon characters, and some brutal Kick the Dog moments for the Tiger side, the conflict instead falls squarely into this.
Cucumber Quest is a more light-hearted variation of this. Characters like Cordelia and the Disaster Masters are pretty Obviously Evil and they don't exactly try to hide it...but their actual interactions with other members of the cast can be surprisingly heartwarming such as Cordelia cheering up her minion Peridot as well as Noisemaster and Mutemaster's unseparable friendship. Meanwhile on the "heroes" side, the Dream Oracle, the supposed Big Good, is portrayed as hilariously incompetent at her job and even interrupts the chapter intermissions whenever they start to question her actions, while Cucumber's father Cabbage is pretty much the personification of a Jerkface, being greedy and teaching his son to do well on tests by cheating. Most of the time it's Played for Laughs.
Homestuck has the conflict between Prospit and Derse, the conflict that drives the "game" of Sburb. Prospit is fighting so that Sburb can perform it's intended purpose, creating new universes, while Derse is fighting to destroy Skaia, which would stop Sburb from destroying innocent worlds and races to propagate itself. In-Universe the players of Sburb are intended to side with Prospit and thus continue the game but it's made clear to the reader that both sides of the conflict are mostly good people. Indeed, late in the Kids session the two armies end up making peace under the unified goal of overthrowing the Black King though this doesn't end well due to Bec Noir...
Schlock Mercenary falls into this quite hard. The main characters are mercenaries who will enthusiastically participate in almost anything as long as there's money in it, while the governments they work for scratch and claw for advantage. Even the most benevolent figure, the Fleetmind, is still extremely ruthless when it needs to be. At the same time, however, most of the people engaging in active bastardry are there for positive reasons such as patriotism, they're just working towards them in horrible, horrible ways.