Dean from Tanya Huff's Summon the Keeper is so well-grounded people instinctively look for roots when they see him. He does housework, never swears, and is really handsome as well. Oh, and he's a twenty-year-old virgin.
In Johannes Cabal the Necromancer: Its part of the Black Comedy tone of the book and how close to being a villain the titular character that his brother, a vampire is by far the nicer guy-he and Frank Barrow (a retired policeman who serves as an antagonist to Cabal in the last few chapters) are the only truly nice guys in the book. In Horst's ideal world, he'd drift from easy job to easy job sleeping with an endless stream of women (later book goes in-depth to explore that Horst is a wholesome womanizer and contrasts him to a more villainous type) and not go out of his way to bother or hurt anybody. Frank likewise would make a traditional Hero in any sort of crime story.
Joshua from Dora Wilk Series is the nicest guy in any given group. He can't stand violence, he works in a school for psychically troubled children, he lets people cry on his shoulder and he's always there for his friends, hiding his own problems from them because he doesn't want to trouble them. On the other hand, Beware the Nice Ones, because when he Manifests, nothing can stop him.
Karal from the Mage Storms trilogy of the Heralds of Valdemar. He's so nice, in fact, that he's terribly ill-suited for the web of political intrigue he's thrust into by the death of his mentor, Ulrich, Karsite ambassador to Valdemar. However, as a priest (and an honest one, even), this very attribute turns out to be his greatest asset in making friends with the Heralds.
Brienne of Tarth. She's kind, generous, honourable and loyal. Unfortunately, these traits are not useful for a woman who lives in a Crapsack World.
Arys Oakheart, being the most unwilling of the Kingsguard to beat Sansa (and does so as lightly as possible), and is steadfastly loyal to Myrcella, whom he is sworn to protect.
Garlan Tyrell is mentioned a few times as a Master Swordsman before his brief appearance at Joffrey's wedding establishes him as a surprisingly nice guy. He's one of the few people who gives Tyrion his due credit for saving the city and makes pleasant conversation with him throughout the procession. He even chastises the king for abusing Tyrion.
Davos Seaworth is one of the most decent-hearted and kind people in the entire series. Though he has been knighted and raised to the nobility by Stannis, being a Working-Class Hero gives him far more insight into the plight of the smallfolk and those most of the nobility consider beneath them, also showing himself to be a loving father and husband (though feels guilty about knowing other woman). Davos remains constantly kind and a Friend to All Children, even going against Stannis' orders by smuggling away Edric Storm to prevent them being burnt by Stannis.
Prince Baelor "Breakspear" Targaryen from "The Hedge Knight" is set up as The Wise Prince, with the potential to embody The Good King. He helps Dunk when they embarrass themselves in front of him, and later acts as one of Dunk's champions in a Trial by Seven, on the grounds Dunk protected the weak and innocent as every Knight should (Dunk attacked Baelor's sadistic nephew Aerion "Brightflame" Targaryen who was torturing a woman). Sadly Baelor dies when his brother Maekar, Aerion's father, accidentally strikes him a fatal blow to the head.
Most of the Stark family, be it Ned, Robb, Bran, or Ned's illegitimate son, Jon Snow — all of whom are honorable, good-hearted, and concerned with doing the right thing. Ned is shown to be greatly respected and admired by the smallfolk under his care, many of whom are still loyal to the Starks, even after many of them have been wiped out. Robb is dutiful and moral and tries his best to do right; Bran — like his father and brothers Robb and Jon — is dutiful and compassionate; Jon is definitely a Stark in all but name and is among the most compassionate and moral characters in this Crapsack World. However, you do not want to piss a Stark off.
Ned Stark's daughters, Sansa and Arya, likewise start out as compassionate and good-hearted albeit in very different ways, with Sansa as a gentle, idealistic proper lady and Arya a down-to-earth tomboy one of the few noble characters in the series not to care about class status, is furious at how the likes of Joffrey mistreat lowborns and risks her life several times to save innocent people. However, their struggles surviving in a Crapsack World begin to train the kindness out of them.
Daenerys Targaryen is likewise kind, gentle-hearted, and compassionate but will retaliate against her enemies.
Jon Snow's best friend, Samwell Tarly, also qualifies as he is kind, open, and compassionate.
Arya's best friend Gendry, despite his surliness is quick to defend the vulnerable, joins the Brotherhood Without Banners because he admires their ideals and was last seen caring for a house of children orphaned by the war.
Isaac Fisher from Outsourced is kind, considerate, and unwilling to take action that could cause future harm. This turns out to be a bad move.
In the Indian novel The White Tiger: Ashok, who is frequently described by Balram as "virtuous."
The Dresden Files: Despite being a holy warrior sworn fight all that will oppress humanity, Michael Carpenter still manages to ooze niceness. He's catholic, but respects other people's choice of religion. He has a large family, every member of which he loves unconditionally.
Brackenfur too. In fact, he's one of the nicest cats in the series.
Billystorm, Leafstar's mate from SkyClan's Destiny.
Shellheart, the father of Crookedstar and Oakheart.
Even Blackstar himself temporarily became this. It causes Lionblaze to jokingly say "Who are you, and what have you done with Blackstar?"
Peeta Mellark in The Hunger Games. Averted a bit in Mockingjay when he is hijacked (completely brainwashed) by the Capitol. He eventually overcomes it, though.
Also, Finnick Odair. Easily one of the most genuinely friendly people in this series.
Harry Potter. Harry is decent and honorable and good, a friend to werewolves and Muggle-borns. He's saved from being boring by also being a brave fighter against Voldemort and the Death Eaters, as well as by having the normal anxieties of a teen boy.
Remus Lupin. He's spent his entire life being shunned and ostracised due to his lycanthropy, but he's never turned against to the dark like so many of his fellow werewolves. Instead, he is one of the kindest, most fair-minded, good-natured people you could hope to meet. This is seemingly averted a little when he tries to leave his wife, Tonks, and his unborn child to go adventuring with Harry. However, his reasons for leaving come from his desire to protect them from the Fantastic Racism they would suffer as the family of a werewolf. He realises the error of his decision after a What the Hell, Hero? from Harry, returning to his family, and is ecstatic with happiness when his son is born.
Neville Longbottom is also noteworthy. He really stands out by being one of the very few fleshed-out Harry Potter characters that doesn't have jerkassery as one of his flaws.
Cedric Diggory, of course. He's in Hufflepuff House, which seems to be the house for ordinary nice guys (and girls). Modest, accomplished, fair minded, chivalrous; Harry finds it hard to dislike him even though Cedric beats him out in dating Cho Chang.
Sofia and Johan Överenskommelser are so close to being flawless and perfect, that they can never cause any drama on their own. But still, they remain close friends/beta couple to the more complex alpha couple Beatrice and Seth.
Ossian Bergman in "De skandalösa" is a Dork Knight and a Gentleman and a Scholar, who seems to be a genuinely nice person. And yet, he's a close friend to the much more complex male protagonist Gabriel Gripklo. And in the same novel, the sweet-natured Proper Lady Venus Dag och Natt is a female example of this trope.
Jonas is intuitive, understanding, sensitive, kind, well-meaning, polite, and wanting to do what's best for the Community.
Fiona is caring and considerate, which makes her a good fit for the job of caring for old people. Although her job of "releasing" old people is not so nice, although she doesn't understand the implications of such an act.
Mason Ashford from Vampire Academy is friendly, pleasant, chivalrous, psychologically well-balanced, and heroic at heart.
Beleg Strongbow from "The Children of Hurin" is a heroic and noble Elf who is Turin's best friend. When they leave Doriath he goes looking for them and joins them in fighting the Orcs. When Turin is captured by Orcs Beleg risks his life to save them. Sadly Turin mistakes him for an Orc and kills him.
Balin the Dwarf seems the kindliest of the Dwarves in "The Hobbit". He is the only Dwarf to enter Erebor with Bilbo, though doesn't go into Smaug the Dragon's lair, and later comes to visit Bilbo. In the Trilogy of "The Hobbit" this is emphasised further.
In Divergent, Al was the most sensitive of the Dauntless initiates, and therefore one of the kindest. Unfortunately, this is what led to his demise.
Lacey from Paper Towns. She comes off as spoiled and a bit shallow, but very, very loyal to her friends and ultimately glad to be friends with Q, Ben and Radar.
Ishmael and Bill from Don't Call Me Ishmael!. Ishmael is friendly to everyone and in the first book of the series he tries to stand up to the bullies making his life hell for a younger boy. Bill is The Quiet One and has a very gentle personality.
Robin from The Girl from the Miracles District is kind, polite, provides a shoulder to cry on, knows when to keep secrets and just beams with niceness, to the point that Nikita spends large chunk of the book suspecting that it's all a very amateur and transparent act.
The protagonist of Along The Winding Road. While Charlotte is necessarily a tough girl after living through the Zombie Apocalypse, she's managed to retain her optimism and does her best to be kind to even the questionable travelers she comes across.
Spirit Animals: Along with Jhi the panda, Rumfuss the boar is one of the nicest spirit animals. So much so that when his bitter master is missing his true spirit animal and a part of himself, instead of showing resentment, Rumfuss gets to the root of the problem and helps him out.
Renegades: So long as his mother's murder isn't concerned, Adrian is the world's purest cinnamon roll, always ready to listen and help out with whatever troubles his teammates. He stops by to cheer up a bunch of kids at a birthday party, helps stray urchins get food and a place to sleep, and has seemingly endless stores of empathy. No wonder Nova falls for him like a meteor.
Rack of the Whateley Universe. He's a dwarf on top of being a mutant, but he has several extremely pretty female friends because he treats them well. And he makes the time to explain to Chaka why she should watch out for the dreaded Sahar.
The superhero Legend, leader of the Protectorate, inspires an almost universal "he's so nice!" reaction in people who meet him, and is generally considered the nicest member of the Triumvirate, with Alexandria being cold and distant and nobody liking Eidolon. As it turns out, he's also the only member of the Triumvirate that isn't aware of the horrible crimes perpetrated by Cauldron.
There's also a twisted inversion of this trope in the form of a villain actually named "Nice Guy." He pretty much renders everyone around him incapable of regarding him as a threat, and most people actually trust him and think of him as a friend, allowing him to calmly walk up to people and start murdering them where they stand, with their friends blithely standing by and unable to do anything about it because he's such a nice guy.
Rajih Assad. He's loyal, chivalrous, and deeply concerned for the wellbeing of his friends.
Lukana Octo is very nice and helpful, even to complete strangers, and often acts as a mediator to settle disputes.
Ayn, who is deeply loyal to his friends and one of the only people in Yatski to treat Clarith well. He even ends up giving his life to get Michaela and Clarith away from the Lucifenian soldiers
Michaela, who is very friendly, kind, and curious, and especially protective of those close to her like Clarith, Gumillia, and Elluka. She does develop a somewhat more snarky personality after becoming the new Millenium Tree.
Ayn Anchor, an honest and trustworthy policeman who wishes to live up to his namesake and protect those in danger.
Nyoze Octo certainly fits the bill, being very kind-hearted and having a strong sense of justice. One of the last things he does is write a letter to his brother Gammon, asking him not to seek revenge against Nemesis should she kill him, knowing she'd only do it because she was forced to.
Lindon is shockingly kind and compassionate considering his upbringing, constantly worried about slaves and workers who are getting hurt by the titanic events he's involved in. His entire reason for becoming stronger is so that he can save Sacred Valley from a coming cataclysm, despite the fact that no one in the Valley except maybe his family cares for him in the slightest.
Eithan dislikes the constant dog-eat-dog nature of the world, where the strong bully the weak and everyone tries to fight everyone else. He has repeatedly forgiven major slights to his honor that he could have used as excuses to execute his enemies, and often uses his omniscience to make minor corrections to make people happier (such as moving a ladder half an inch so that it won't fall).
Johnny Smith from The Dead Zone is extremely nice, concerned about others, excited about teaching, and so obviously well-meaning that it's impossible to hold a grudge against him. Even after it becomes obvious to him that [[spoiler: the only way to be sure of averting nuclear holocaust is to kill Greg Stillson, he procrastinates and delays as long as possible because murder is wrong.
Art of Flawed , though a bit cowardly at times, proves himself to be a truly good person who cares about Celestine, even after they have an argument.
John Segundus of Jonathan Strange & Mr Norrell is such a nice guy it hurts. He writes an article praising Norrell even after the man destroyed his livelihood because he thinks it's for the benefit of English magic, he's willing to defend Lady Pole with his life and ends up being the first person to realise she's under an enchantment, and as a result he's the only magician that Lady Pole can actually stand. The Narrator lays it on thick at times, but he really is just that nice, and it's demonstrated so clearly through his actions as well as descriptions that it can be easily forgiven.
Narrator: For who can remain angry with Mr Segundus? I dare say there are people in the world who are able to resent goodness and amiability, whose spirits are irritated by gentleness - but I am glad to say that Jonathan Strange was not of their number.