Anderson plays this role for the Vatican side- he may love fighting monsters, including Seras, but he does stick to his sense of right and wrong even as his faction reaches new lows—culminating in his destruction of Maxwell's anti-zombie shelter when he realizes the latter has gone around the bend.
Starrk ends up being a deconstruction as his fight with Shunsui shows that even though he was a noble person, he was still fighting on the wrong side. And Shunsui kills him for it.
Also, Riruka Dokugamine, the only one in Xcution who doesn't want Ichigo's powers that Ginjou promised to share with the other members and tries to reject it. It helps that she actually befriended Ichigo and Orihime genuinely.
The Twelfth Division from Soul Society is full of... very morally ambiguous people, to say it politely. This doesn't seem to be the case with Rin Tsubokura, as there's no word on him having been involved in the Quincy experimentation while we know that Mayuri, Akon, and Hiyosu participated in it.
Sixinglong/Nouva Shenron in the last arc of Dragon Ball GT. He's a Martial PacifistNoble Demon who believes in Honorable Duels, and goes as far as to put off his fight with Goku when he's temporarily blinded. Justified because he came from the only selfish wish made by the Dragon Balls in the series, giving King Piccolo his youth back.
Mikiya Kokutou from Kara no Kyoukai is a really decent guy and a devout Zen Buddhist. The people he hangs around with are... neutral at best. He comments on how he'll just have to share the karma of Shiki's sins to be with her. Miraculously, he does this without sounding like a jackass.
In One Piece, we have Hachi who was the least cruel out of Arlong's pirates. He would in fact become an ally to the Straw Hats later.
Though later chapters would show more good (or at least not corrupt, an arrogant Jerkass or a fanatical Knight Templar) Marines, Smoker and his partner Tashigi are the very first named Marines to be depicted as such in almost 100 chapters.
Tobi seemed like this at first - a complete Cloudcuckoolander even next to Dark Chick Deidara, he was at least as interested in having dango with his partner as being evil. Then the entire thing turned out to be an act.
Kisame: Don't get me wrong, I liked Tobi. He managed to lighten the mood of this rather gloomy organization.
Before Maia joined, Shizuka might count since she doesn't cause the same damage as the above. However, she never has a problem with what they do either.
A Certain Magical Index has Acqua of the Back, the only truly noble member of God's Right Seat, who genuinely wants to help and protect the world. The other members are corrupt and/or have secret agendas.
In an excellent example of having both a Token Good Teammate and a Token Evil Teammate on the same team, the Black and Gray Morality world of Slayers has Amelia and Xellos respectively. The rest of the team tend to be selfish jerks (especially Lina), but Xellos admits to being evil and tags along because a.) he's under orders to, and b.) it's just fun. Amelia, on the other hand, is Wrong Genre Savvy and thinks she's in a Magical Girl show, even going so far as to trying to cure Xellos of being evil through the power of love. The rest of the team swings back and forth along the spectrum of good vs evil.
To some degree Togusa in Ghost in the Shell counts. The rest of Section 9 is fighting terrorism and organized crime, and government corruption at times, and are devoted to protect the citizen from major threats. However, Togusa is the only one who would risk the trouble of apprehending armed criminals alive and see that they are properly tried. Everyone else strikes first and starts looking for any survivors that can be questioned after the dust has settled.
Though everyone from the Sabertooth guild in Fairy Tail is cocky, Rogue is the only one to actually voice his distaste at how they humiliated and expelled one of their members over a single loss. It's an incredibly stark contrast with his close companion Sting's amusement over the poor girl's weakness.
After Master Gienma and Minerva, the two evil members of the guild left Sabertooth and Sting took over the master position, the guild loses its Jerkass attitude, but Rogue has the potential to become evil like his future self.
Yu-Gi-Oh!: While all of Dartz's elite minions have tragic backstories that explain their Start of Darkness, Raphael is distinct in that he seems to genuinely believe that Dartz is saving the world. He has so much respect for and connection to his cards that he successfully uses the Heart of the Cards against Yami Yugi. He also successfully fights the influence of the Orichalcos, something only Mai had previously done (with The Power of Love) and subsequently rescues Mai and Valon's comatose bodies from an earthquake.
Victoria Hand. Out of everyone on the team, she's the one person who isn't a homicidal maniac. So much that when Captain America is appointed to Osborn/Stark/Fury's old position he makes her his New Avengers liason
In a later incarnation of the team composed mainly of unrepentant criminals, the good teammate was Songbird. In the version of the group after that, Norman Osborn's private black ops task force, the good teammate was Paladin, though he wasn't so much "good" as "not bad." Eventually the Headsman, Ant-Man, and the Ghost joined him — though it was Ghost who made it all possible.
Lucas Lee of the Evil Exes in Scott Pilgrim is not a Jerkass like much of the other Exes. He turns out to actually be a decent guy who is genuinely friendly to Scott. However, Scott still has to defeat him to free Ramona from the Evil Exes' control.
He was more of an antagonistic Jerkass in the film adaptation, however.
Played for Laughs in Uncanny X-Men vol.2, when Scott creates what he calls "Extinction Team" - a group of the most powerful and dangerous members of X-Men to perform large-scale heroic acts, as a warning to everybody willing attack X-Men by showing what can they do. He even directly calls them weapons of mass destruction. The team is made of himself, Storm, Hope, Emma Frost, Colossus (who had recently became The Juggernaut), Magik (frequent Token Evil Teammate of New Mutants), Sub-Mariner and Magneto. Storm points out that in entire team only her, Hope and Scott haven't been, at least once in their life, supervillians and considering he just compared X-Men to North Korea, he doesn't count.
Suishoku in Shining Pretty Cure. He's actually a pretty nice person from the start, he resolves to Never Hurt an Innocent (unlike the rest of the Shade Quartet, who pick up victims wherever they can get them) and the only reason he's even working for the bad guys is because of his devotion to the Queen. Strangely enough, it's not he who is moving towards a Heel-Face Turn, but rather, Amazora. Both are slated to turn good in the second half, and Amazora makes the turn first, with him coming second. The other two in the Shade Quartet follow suit right before they die at the hands of Meran and Korii.
Played With for Jessie, James and Meowth in Pokemon fanfic Symbiosis, while they are largely innocent and misguided, they are still just as dangerous as the rest of Team Rocket.
The Harry Potter band The Parselmouths are, in-universe, two Slytherins who were eventually joined by a Gryffindor (mostly because the Slytherins wanted someone to do the work for them). Summarized here:
In Mr. Smith Goes to Washington, Jefferson Smith is the nicest, greatest guy in the world, and everyone around him sucks. But by being around him, they start to get better. Ms. Saunders the secretary, the Corrupt Senator from Smith's home state, they all see the light.
The Amish family in Saving Sarah Cain are this in public school. In their case they make venial compromises that understandably irritates Big Sis Lyddie (who is THEIR "Token Good Teammate").
In The Gamers 2, the GM sends along a paladin in order to keep in check the group's more sociopathic members. All it does is have them find more creative ways to be sociopaths.
Jim Caviezel's character in The Thin Red Line, Witt, is so noble and idealistic that he comes across as jarring to the other soldiers around him.
Charles Bronson's character in The Dirty Dozen is the most reliable of the bunch, with Maggot on the other side of the spectrum as the Token Evil Teammate.
Isabelle in Predators. She's a mere Israeli sniper alongside a mercenary, enforcers for Yakuza, RUF and Mexican cartels and a death row murderer (and a doctor who's actually a serial killer), and is usually the only one with some conscience in the team.
Nikolai the Spetnaz soldiers counts too, being a friendly family man who sacrificed his life to save one of the group for no reason but it being the right thing to do.
Professor Hugo Fassbender in The Pink Panther Strikes Again, who wanted nothing to do with former Chief Inspector Dreyfus' reign of terror, as he doesn't believe in world domination, but had no choice when Dreyfus tortured his daughter Margo. He unwillingly joined with Dreyfus to build a doomsday device to threaten the world unless they kill Chief Inspector Clouseau.
Subverted in Stoker in which Whip Taylor seems to be this among his Jerk Jock group of friends who harass India—telling them to leave her alone, apologizing for their behavior. To that end, she seeks him out late one night to talk. . .and he tries to rape her when she rebuffs his advances.
In Dogma, the unnamed female board member (played by Linda Levine) is the lone innocent on the Mooby board of directors.
Deejay: Are you totally demented, man?! Bison is the enemy of freedom and peace! These people have come from all over the world to stop him!
Zangief: Bison?! He's a... bad guy?!
Loial the Ogier in The Wheel of Time series. Most of the 'good guys' are just as likely to act in their own self-interest as help their friends and allies, even when cooperation is vital. Loial sometimes finds himself caught between these squabbles, but he cares deeply for all of his friends and is typically much more willing to risk his neck for them than they are for each other.
David Balfour in Kidnapped. Though the difference is more ideological then moral it is easy to mistake one for the other and he can be self-righteous.
Túrin spends some time among outlaws in Lay of the Children of Húrin.
Wintrow in Robin Hobb's The Liveship Traders trilogy tries hard to be this, but is mostly ridiculed (or worse) for his high moral standards. Amber manages better with her views on slavery, violence and the treatment of Paragon.
The Geste brothers in Beau Geste. They are Gentleman-rankers among rather ruffianly Foreign Legionaires and some of this is class difference. However they do, to some degree try to be the Token Good Teammate. Like the good English boys they are.
Patrius in the Farsala Trilogy, though one could argue that it's only really noticeable when he is contrasted with his commander, Garren.
Though she only appears briefly in one scene in the original novel, Bree Tanner is this for Victoria's newborn army in the Twilight series. The film adaptation expands her role significantly and especially emphasizes this aspect of her character.
Although her actions in her novella make this a case of YMMV. Arguably Freaky Fred is closer in that story, seeing as he's the only newborn who actively refrains from the fighting between newborns and defends Bree from them.
Thomas Raith qualifies as the token good member of his family in the early The Dresden Files, as the only Raith with anything resembling morals. Then he leaves the family.
Subverted with great gusto in The Blending series by Sharon Green. The team of Psycho Rangers set up in contrast to the main characters appears to have a token good member and Only Sane Man in the person of their Spirit wielder... until he reveals he's been using his power to control the other members of their team and is probably the most evil of the five - and the most ambitious - just a lot smarter and less obvious about it.
Nate Ford to the rest of the Leverage team. He was specifically hired to be the "one honest man" on a crew of thieves. However, the distinction gets fuzzier as time goes by, as Nate begins to almost relish his role of criminal mastermind and the rest of the team discovers they enjoy using their skills to help people. Sophie especially is pointed out to be his moral compass later in the series.
Lisa is becoming this on V-2009, which is very bad news considering her mother is the Big Bad
Joshua is probably a more clear-cut example of this, at least until the season 1 finale.
Gai Ikari, Gokai Silver, is another one, as he's an Ascended Fanboy of Super Sentai who wants the Gokaigers to do things like help children who've tripped and give encouraging messages to their fans. Notably, when he's imagining what he wants the team to be like, Ahim's the only one who actually still acts like herself. In a surprise, not only do the Gokaigers think his imagination is ridiculous, even Ahim thinks his version of herself isn't exactly cool (though in the most polite way possible of saying it)
Don Doggoier AKA Doc, is another one, though still fits a little more than Ahim since his main draw is that he's a Reluctant Warrior, thus less bloodthirsty than the rest. This does comes with a price, though, he's the designated Butt Monkey, so much that in Gai's Imagine Spot above, Don is nonexistant and had his place taken by Gai.
Cosmo Kramer from Seinfeld is the only one of the four main characters who is consistently shown to have a conscience. While he slips up every now and then, he almost always tries to lend a helping hand to people in need. Unfortunately, many of these attempts fail and make things worse.
Behrooz Araz served as this to the antagonists during the fourth season of 24, which included his own parents. He was consistently on the fence about helping them since it meant the deaths of several innocent people, and the last straw that proved he just couldn't work well with them was when they wound up killing his girlfriend. This eventually led his own father to try and kill him as well.
The Secret World of Alex Mack has the titular super-powered protagonist hiding from Danielle Atron and Vince her chief of security, both of whom want to experiment on and/or kill her. Also working with them is Nice Guy Dave, the trucker who caused the accident that gave Alex superpowers. He only wants to catch her because she was exposed to an unstable chemical and wants to help her. When he figures out the truth, he keeps it to himself, having overheard Atron's real plans earlier.
Buffy the Vampire Slayer had Jonathan of the Nerd Trio during its sixth season. Whereas Warren proved himself to be a bastard and Andrew (at the time) was just a suck-up who sided with either of the other two when the situation proved best for it, Jonathan was the only one of the trio with a true conscience and never wanted to actually kill Buffy, even going against Warren several times when he attempted to do so. When Warren winds up killing his ex, this is what goes on to drive a permanent wedge between him and the others, ultimately leading him to betray Warren by revealing the weakness in his newest plan to stop Buffy late in season six.
During One Life to Live's infamous gang rape storyline of 1993, one of the three rapists in question, Powell Lord the III, was repeatedly shown to be the only one who had any remorse over what they had done. Indeed, he's bullied by the other two into participating and is so plagued with guilt that he eventually tries to kill himself before finally pulling himself together and confessing. However, a year later, it is revealed that he is the serial rapist who's been terrorizing the local hospital, leaving viewers to wonder if his guilt drove him insane or if he was secretly like this already before the gang rape unleashed the demon lurking inside.
When the World Wrestling Federation was invaded by WCW and ECW, Gregory Helms joined WCW's ranks as a standard villain. He soon became the comical superhero character The Hurricane, who was polite to his opponents and eschewed typical heel tactics. After the WCW/ECW Alliance folded, he became a beloved good guy nearly instantly.
A not uncommon position given the high popularity of supposedlyChaotic Neutral characters among Munchkins and Real Men. This puts anyone in the party actually interested in roleplaying in a very uncomfortable position.
In parties that are actually supposed to be evil, someone tends to end up as this, at least relativelyspeaking.
In Magic: The Gathering's Scars block, we see the colors slowly become remade into Phyrexia. (Think the Borg meets the Zerg, with enough Body Horror to go around.) Black is completely Phyrexian in the last set, but red is the last one to be Phyrexianized, because red, being the color of individuality and emotion, is the least Phyrexian. Not surprisingly, red's praetor, Urabrask the Hidden, is the only one of the five that can feel anything akin to compassion. So we get flavor text like Priest of Urabrask and, perhaps hinting at the far future, Urabrask himself.
Beltway and Lupo to the rest of the Wolfpack in Resident Evil: Operation Raccoon City, to a very loose definition of "good"; they're still remorselessly hunting down innocent cops and civilians, but their lack of overt psychopathic tendencies still puts them over the mark compared to the rest of their team.
Ada Wong in RE4, if you count Wesker and the people working for him as a team given how little actual teamwork happens. She spends enough time and effort helping Leon that you can almost forget that she's trying to get the Dominance Plaga for Wesker until she steals it from Leon at gunpoint. Though it's revealed that she gave Wesker a fake Plaga and gave the real one to her other employers.
Baldur's Gate 2 only has three Evil-aligned NPC that can join your party. If you made your PC evil, then Imoen will be your Token Good Teammate since she's Neutral Good. If she's not on your team, then whoever is Good or Neutral alignment becomes your Token Good Teammate.
Throne of Bhaal has Balthazar, a Lawful Good monk who has teamed up with the bad guys to accomplish the goal of destroying what he sees as a great evil. Interestingly, the group itself is a part of that evil and he plans to see the entirety of it destroyed — himself included — in the end.
In Planescape: Torment, Morte the flying talking skull is only good-aligned character in your neutral-aligned party. You may also become good, but it'll require some time.
Flonne in Disgaea. Originally joins to understand demons and teach them about love.
Legacy of Kain : Janos Audron for the vampires. Kain is a Magnificent Bastard out to achieve his goals by any means necessary. Vorador is a sadistic hedonist with a penchant for torture. Raziel, while not really evil, can be indecisive, self-righteous, and is mostly motivated by wanting to save himself. Janos, on the other hand, is a kind, fatherly cleric type who is one of the few people in the games who will tell the truth in a straightforward, artless manner. He even thinks kindly of the murderous Sarafan, believing that they're only acting out of fear and ignorance.
To a lesser extent, Judge Magister Gabranth. In the 13th cycle, he's nothing more than a disgruntled jailer who serves as a warden for those no longer used in the conflict. Several of lines are somber and hint that he wants nothing more than penance for his past transgressions, while most of the other Chaos warriors mock him for his more admirable qualities. Compare this to Shantotto, who serves as Team Cosmos' Token Evil Teammate (to the point that most of the villains revere her). Both of these are somewhat subverted in the prequel Duodecim, as the two are actually affiliated with their respective deities this time around (however, Gabranth just seems to be doing his job and seems to be confronting Cosmos simply to end the war—thus lacking an ulterior motive unlike most of the others, while Shantotto is still a fair bit malicious, even towards her ally Prishe).
Also, Kuja is a bit of a tragic case. He's actively working with the heroes Bartz, Zidane, and Squall, up until Kefka intervenes. He's even responsible for Cloud's Heel-Face Turn and Terra's too. After he's defeated by Lightning, Kefka implants false memories to ensure his full on villainy in the Thirteenth Cycle.
In the end of BlazBlue Continuum Shift, Litchi ends up joining NOL as the Token Good Teammate. Unlike all other who directly served the Imperator, the reason why she joins was because her body condition got worse and the only one who'd want to give the cure for both her and Arakune is NOL, thus she has the least loyalty to the NOL and was only there for necessary self preservation and saving a beloved. Also in Chrono Phantasma, she didn't undergo any Evil Costume Switch and retains her sane personality, thereby making her squarely on the trope.
Both Rei and Shuu/Shew becomes this in Hokuto Musou Dream Mode, on basis that the antagonist is the Nanto side, and they're both Nanto practicioners. In the real story, they would've been Kenshiro's greatest allies.
Leo in Final Fantasy VI is also a known case of this as well in fact the game likes to lampshade the fact that the only reason why Leo is considered a antagonist is only because he works with the Empire.
Cao Ren in Dynasty Warriors. In a game where Wei stores A LOT of scary looking, ambitious, jerkwad or scheming people... we got this peaceful shorty guy who just wants the chaos to end. And this is before Wei takes a swing in Anti-Villain-y since the 6th game.
And in the 7th game, even if Wei is just merely Designated Villain, one look at serene, compassionate poet/musician Cai Wenji amongst Wei would make you agree that she's another Token Good Teammate.
In Warriors Orochi, Himiko is mainly on the side of the forces of Orochi because Da Ji acts as a Cool Big Sis toward her. When she and Da Ji are captured by the Resistance in Warriors Orochi 3, Himiko gets along better with the Resistance fighters (as unlike Da Ji, she doesn't have an ulterior motive for doing so), and goes along with a few of the girls in one Side Quest to help rescue another of their missing warriors.
Also in 3, Mouri Motonari is also one. He's cunning enough to realize that the balance of the dimensional world actually depends on Da Ji's presence, like it or not, so he protects and joins forces with her, despite still being the jovial laid back guy (as compared with his dickish self in Sengoku Basara which wouldn't make him this trope), if you compare with those used to align with Da Ji (except Himiko above) like Masamune, Fuuma, Keiji, Achilles or Dong Zhuo.
Mina Tang in Alpha Protocol. The only employee of the eponymous agency who seems to have any sort of conscience, and also the only one of Mike Thorton's Mission Controls who care if he kills American agents or civilians, makes deals with arms traffickers, or commits similar acts of Dirty Business.
Though over the course of Character Development the others have become slightly more Good due to his influence and Cale has become less idealistic.
In The Order of the Stick the Linear Guild usually has some. Not surprising as they are the evil opposites of the Order, which has Belkar as the Token Evil Teammate. The original Linear Guild has Hilgya, a priestess of Loki, who turns out to be not overly malicious (though she repeatedly attempted to murder her husband. While it being an arranged marriage may complicate things, her husband seemed to be a nice guy who did his best to make her happy, and murder was her first solution rather than the more successful fleeing she did later). Later they recruit a Lawful Good (or at least honorable Lawful Neutral, considering he let Nale and crew get away with mass murder) kobold to serve as the counterpart to Belkar.
Artie from Narbonic normally preoccupies himself with the support of hippie-ish causes (such as world peace and the election of Dennis Kucinich), all while living with a mad scientist and her henchmen.
Come Skin Horse, he's become an activist for transgenic rights.
In The Guild, despite the team name of "The Knights of Good", Codex and Vork are the only ones who seem to quest with anything but loot in mind. Then we find out how Vork gets his electricity and internet access by stealing it from his Alzheimers-afflicted neighbor. Offline Codex is the only one who isn't either self-centered or completely divorced from reality.
In Red vs. Blue, the eternally cheerful Donut seems to be the only Blood Gulch soldier who doesn't openly despise the rest of the crew. The series' Designated Hero Church even remarks that Donut is harmless and probably wouldn't hurt a fly (this is in spite of the fact that he actually killed his [admittedly, tank-driving, out-for-blood, mercenary] girlfriend). Everyone else on either team are various mixes of apathy, misanthropy, and Comedic Sociopathy. Even the easy-going and friendly Caboose secretly harbors a huge dislike of Tucker, as well as a tendency to accidentally kill his own teammates.
Doc. It's especially hilarious because the other members of his team consist of: a bomb, a robot's head, and an AI that's taken control (mostly) of Doc's armor.
Yvan Viau aka Labyrinthe of the ASH universe is canonically the token good teammate on the Conclave of Supervillains.
Now that he's gone (very likely dead), Nella is back in the role of the only regular person there with a listenable conscience.
Exaggerated completely on Jimmy Two-Shoes, where Jimmy is the Token Good for the whole city.
Zuko's Uncle Iroh in the first season of Avatar: The Last Airbender; he's a former Fire Nation general who had a pre-series Heel-Face Turn and only helps his nephew hunt the Avatar so he can look after him.
John Canmore is always arguing against his siblings' single-issue wonk against the Gargoyles. And then the trope is subverted, BIG TIME.
Played straight with Dingo. Of the five members of the Pack, he's the only one who doesn't trade his humanity for super powers (he goes with a Battle Suit instead). He's also the only one whose Heel-Face Turn occurs for truly altruistic reasons.
More than that; he's apparently the only person on Earth who is not on Santa's naughty / target list, meaning that Santa sees Earthlings as My Enemies And Zoidberg.
From Jem we have Stormer of The Misfits. As an example, when The Misfits discovered that the Holograms had to perform in a movie alongside them, in order to raise money for an operation one of the Starlight Girls desperately needed, the band is thinking up ways they can screw with Jem. However, the first words out of Stormer's mouth when she finds out is "Which little girl?"
Recess: Miss Grotke is this among the faculty members, though downplayed as they aren't "evil"- they're just doing their jobs and are portrayed as the antagonists for most of the episodes. While most of the faculty are apathetic or extremely stern, she's sweet and easy-going, and always stands up for the kids.