Liara and a paragon Shepard are seriously nice as well.
Believe it or not, Miranda has become this by Mass Effect 3, having absolutely zero Kick the Dog moments, practically begging Shepard for forgiveness for desiring to put a control chip into them at the beginning of 2, and going further than ever to protect her sister from her father and in the process, warning innocent civilians about Sanctuary.
In the sequel there is the Disciple, who is also a possible love interest for the female PC.
In both series the main PC can be played as such, specifically in the second game where the Jedi become the Hero Antagonist in comparison to a moral, just, and kind Exile.
The Main Character in Persona 4 almost never speaks, but he seems like a really nice person, both in his few dialogue choices (always polite, considerate, and caring) and in action (helps almost everyone whom he meets overcome their psychological issues, works at a daycare center, hospital, and a tutor).
Also the Male and Female Protagonists from Persona 3.
Rise Kujikawa from Persona 4. Notable, because you'd pretty much expect her to be very Tsundere when you first see her. Twin tails, Zettai Ryouiki, one of the female leads and a love interest, voiced by Rie Kugimiya in the Japanese version... you get the picture. But not only is she not a Tsundere, she's even been described as the anti-Tsundere. She's bubbly, outgoing, a gigantic flirt and acts quite down-to-earth despite being a famous (former) Idol Singer.
It's saying a lot when the nicest character in such a bleak story turns out to be the most evil character.
Dragon Age: Origins's Alistair is about as nice as is possible to be, unless you hit his Berserk Button. Leliana is very sweet, and even Zevran, despite being an assassin hired to kill you, is good-natured and easygoing. Not coincidentally, they are three of the four potential love interests in the game.
The nicest characters in Dragon Age II are Merrill and Varric, mostly because Merrill doesn't really get how or why to be mean to people and Varric limits himself to poking fun.
Varric never goes anywhere without Bianca, and we all knows that she is as vicious as he is snarky
There's also the PC's sister Bethany, who very much lives up to Varric's nickname for her: Sunshine.
Bartz from Final Fantasy V is one of the few protagonists in the series who is just nice, with no underlying issues or moments of Jerkassery. He's caring towards his fellow Light Warriors, very easygoing, and acts as a brother figure to Krile when Galuf dies and she takes his place.
Zack Fair, from the Final Fantasy VII prequel Crisis Core. He's upbeat, sincere, utterly loyal, completely adorkable, and just wants to be a hero (in the very best sense of the word). Because of this, he manages to make friends with practically everyone he encounters, including Shrinking Violet Cloud, the Turks and pre-Nibelheim Sephiroth. Contrast to how Cloud, the main character of Final Fantasy VII, starts out his story as a vain, arrogant, apathetic asshole who deliberately antagonises his employers, and earns either fawning admiration or loathing from everyone around him until he grows up a little.
Genki Girl Moria from Fallout 3 is one of the few people in the game that is not an obnoxious asshole who urges you to kill him, also, most ghouls in their town.
Of course, during her sidequest, she pretty much encourages you to expose yourself to near fatal amounts of radiation, and severely injure yourself. All in the name of research, of course. And you don't actually HAVE to do it, you can instead just crush her dreams and leave her horribly depressed. Or you can nuke her hometown and leave her as a radioactive ghoul... You Bastard.
Paladin Hoss is genuinely grateful to a Good Karma Lone Wanderer who helps him out, giving praise and promising protection.
Atrus from Myst is friendly, helpful, peace-loving, wise and sensible.
Guy from Tales of the Abyss is charming, laid-back, patient, and mature. In a world where all major characters have Dark and Troubled Past, he is the only one who manages to move on and thus grows up to be genuinely cheerful and all around pleasant simply rather than becoming jerkass, angsty, suicidal or omnicidal like the other characters (except Mieu). Other characters and especially girls notice, lampshade, and take advantage of his nice guy qualities though, much to his chagrin.
Stefan Bekowsky from L.A. Noire is this compared to the rest of Cole's partners, who are a (somewhat loveable) sexist, a despicable Smug Snake, and a WW1 vet with an initially abrasive attitude. Bekowsky himself? His worst flaw is occasionally flirting with female victims.
Tails of Sonic the Hedgehog is easily one of the nicest characters in the cast, and is even perfectly alright with accepting Eggman as a friend if he doesn't have an evil scheme at the moment.
Cream the Rabbit is also very friendly, befriending the formerly distant Blaze the Cat, which allowed her to start working with Sonic and avert a multi-dimensional calamity.
Similarly, Mario and Luigi from Super Mario Bros.. They're very open, compliment people they're competing against, and overall help anybody with a problem they can solve.
In Mario Party 3, Star Stamps reflect the character's personality. Luigi can get the Kindness Stamp along with most of the other Stamps.
Even though Donkey Kong is a pain in the arse for Mario in Mario vs. Donkey Kong, when Donkey Kong starts sobbing because he can't get his hands on any of the toys, Mario just says, "It's OK, don't cry!"
Isaac was openly identified as a Nice Guy by the extras for the first game, since he's a Heroic Mime in that one. Then in The Lost Age, he got to speak for himself, and he was good, but not very nice. The shift might be justified by all the crap he went through in the first game and the pressure he's still under in TLA, but it was still pretty jarring to a lot of players.
Ivan was identified as a sweet kid, but had some issues with Mind Over Manners even in the first game, which he was even called out on.
Mia has a little bit of Deadpan Snarker, but is mostly a gentle White Magician Girl and the first truly nice player character in the series. Her Establishing Character Moment is healing an elderly couple, she quickly puts her trust in Isaac's group despite the doubtful circumstances of their meeting, and her most aggressive moment is even fully merited - revulsion with her cousin, Alex, upon realising the extent of his betraying their Clan's ideals.
Piers in The Lost Age is probably the first genuinely nice male player character. He's initially standoffish due to some trust issues, but once he defrosts, he is quite mellow and gentle. Heck, his Establishing Character Moment scene even has him try to comfort and empathize with an abuser, and mentally kicking himself after he's been driven to lash out with his Psynergy.
Dark Dawn's Matthew is generally held to be a sweet guy, though being as he is the son of the aforementioned Isaac and a known pottymouth, this might need to be taken with a grain of salt.
Amiti on the other hand is completely transparent, and pure sugar. Even to the nation presently at war with his. He's just that nice. It's a genuinely shocking moment when he first voices his opinions on criminal justice, and even then, he calms down after a gentle reprimand and a reminder of what's at stake.
Sveta of Morgal is so far the straightest example of this trope (even though she's not human, but a Beastwoman. She leads the party despite only just meeting them, helps them even when their goals come into opposition with her country's leader, Volechek (who is also her brother), protects the lives of people to be executed as part of her country's festival, and does her part to save not just her own people but the whole world. She's also an Action Girl who isn't passive-aggressive, and recognises that she can't leave the Grave Eclipse running for a second even though it would kill her brother, because to do so would only kill more innocent people.
Dr. Petrovich Madnar, who is a scientist and family man. He was forced to build TX-55 because his daughter is being held hostage.
Gustava Heffner, who joined Czechoslovakia Secret Police to atone, after she denied asylum.
Hal "Otacon" Emmerich. A nerdy otaku, kind, believes in people. Build Metal Gear REX since he believes that it's a anti-nuclear weapon.
Dr. Nikolai Sokolov. He only build Shagohod under Volgin's threat. A nice guy and loyal family man (he cares for Tatyana despite she's not his lover, and he mentions that he only had one lover, his wife).
The Sorrow. He willingly died so that his lover and child could survive. He did mess with Naked Snake at one point, but he only punished Naked Snake for atrocities he done, and it's skippable. And he keeps giving hints to Naked Snake during the game.
Similarly, Gears of War has, most notably, Dom Santiago, all three Carmine brothers shown, and Cole, of the main cast, along with Dizzy and Anya of the supporting. Baird is a Deadpan SnarkerInsufferable GeniusJerk with a Heart of Gold and Protagonist Marcus is a Knight in Sour Armor, stopping them from fulfilling it, along with Sam, who like Baird is too much of a Deadpan Snarker to qualify, but the above mentioned main Nice Guys, likewise, have bad things happen to them. Dom lost his brother and children before the game series to the Pendulum Wars and E Day respectfully, his wife ran out and went missing, then e later found her and had to Mercy Kill her due to her torture leaving her catatonic. Anthony and Benjamin Carmine both died in battle, meaning Clayton lost two of his younger brothers, and Cole lost his entire family before the game, and off-camera during the opening levels also lost most of his squad.
BlazBlue is rife with folks of decent temperament, though some take a bit of work to get through their emotional defenses. Whether it's Ragna, Noel, Bang, Tager, Makoto or even Antivillains like Litchi and Tsubaki, one can find someone who can lend them a shoulder if they know how to get to them. It's not just these examples, either - generally, any named character (and even some unnamed ones) are people you won't be blamed for wanting to hang around with unless they go by the names YuukiTerumi, ReliusClover, Imperator Librarius, or Azrael* though this last one may be open to interpretation due to lack of story info.
Resident Evil 2 has Leon S. Kennedy; rookie cop, first day on the job, and is thrown into a Zombie Apocalypse. He devotes his strength in getting Ben (a reporter) out to safety and making sure Ada is out of harm's way (even taking a bullet for her). This gets Leon viewed as naive and gullible by the other characters in the game; Ben thinks Leon is just a cop who doesn't know what's really going on (Ben gets killed later on) and Ada sees Leon as dead weight to her mission (at first). Even Claire tends to ignore Leon at times. Leon becomes a Deadpan Snarker by Resident Evil 4, but never gives up in trying to help and protect others.
Addressed in the novels: When Ada attempts to flirt with him he admits he's scared and ignores the fanservice before saying he just wants to be a good cop. She's duly impressed.
Most of the younger female cast members of the Street Fighter series are pleasant and good people (Sakura, Ibuki, and Elena especially). This is why Juri's introduction in Super Street Fighter IV was such a shocking contrast, because up to then Capcom had never introduced a female fighter who wasn't a Nice Girl (Juli and Juni in Alpha 3 were antagonistic characters but only against their will; Chun-Li, Viper, and Cammy are determined, focused, and somewhat militant but also good-aligned characters).
Giorno proves he is as sweet and kind as his biological father Jonathan in the "what if" DLC scenario for Vento Aureo in JoJo's Bizarre Adventure: All Star Battle. Fugo found out about the deaths of Narancia and Buccerati after his cowardly abandonment of his friends at San Marco Cathedral in Venice. Blaming himself, he comes before Giorno, now the Boss of the Italian Mafia, and begs to be taken back into the family. Giorno summons the Godlike Gold-Experience-Requiem and challenges Fugo to prove his dedication by defeating him in this state. If you somehow win this fight, Girono reveals that he holds no grudges for your betrayal, and embraces you once more as as friend. To this Fugo furiously wept Manly Tears, and this time pledges his "body, heart and soul" to Giorno for life. Just like his father Jonathan, Giorno is kindness personified.
Kennen from the Kinkou Order. Justfied as he's "The Heart of the Tempest". Heck, he's even willing to forgive Zed as well.
Zac was designed by Zaun's Mad Scientists, originally as a super soldier, where is taken care by two-caring husband-and-wife scientists as their own child. Despite all the trauma and the original purpose of Zac, he's happen to a nice guy at heart who serves as a defender of the helpless and the innocent.
Teemo happens to be a very friendly yordle scout. May overlap of Beware of the Nice Ones since he can be a cold-blooded assassin when on-duty.
Braum is so far the champion of Nice Guy in Runeterra. Not only his quotes are all nice, friendly and encouraging even to his enemies, his play style revolve around defending his teammates and helping them out. His lore has zero tragic elements as well, he just happens to be that kind of nice goat herder with immense strength, determination to help people in need. And he quotes his mom's words very fondly.
His introductory video features his intervening to save a poro from a hail of arrows.
Your partner in each game of the Pokémon Mystery Dungeon series is always one of the brightest, most positive characters in the story, and they make that immediately apparent by how readily they decide to befriend and look out for the hero just moments after they meet.
Gates To Infinity has a rather unexpected example in the form of Hydreigon, who's instantly likable from the moment you meet him in person, having a polite and kindly manner that runs entirely contrary to what one might expect from a member of his species.
Oscar is easy-going and polite to everyone even when they annoy him. He's also remarkably self-effacing for all his talents.
Rhys consistently shows great concern even for complete strangers and never bickers with anyone, even when they're pulling dangerous stunts.
Zihark is friendly to all the people he meets, and is only willing to criticize others' behavior when it starts hurting other people. He doesn't even have the heart to directly reject Meg.
Ranulf is an easy-going egalitarian who quickly becomes very chummy with Ike for this reason.
Jorji Costava from Papers, Please. During the game, you will have to reject or detain him several times, and there only are two occasions in which he is actually clear to go. But even if you reject him in those occasions, he will still direct you to a forger that can help you flee Arstotzka, should you need to.