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.
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.
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 (essentially brainwashed) by the Capitol. He eventually overcomes it, though.
Also, Finnick Odair. Easily one of the most genuinely friendly people in this series.
Remus Lupin in Harry Potter. 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.
Harry himself might count as this, especially in the early and the last book. He is unambiguously heroic and good.
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.