Facebook has 7teen, a spinoff to 6teen, and it introduces Jonesy's dad, Michael, as one of the most friendly, compassionate, reasonable, level-headed and fatherly (whether you're his kid or not) parental in the series. Though Jude's dad, Justin, fits this trope as well, even in spite of being the Deadpan Snarker of the family.
Cinderjuice and its sequels have Prince Vince, who long ago gave up any possible hope of becoming Lydia's Love Interest. Instead, he uses his Tumblr account to help the heroes. He reads the story chapters as they get posted online and uses what he learns to send food, supplies, and other forms of assistance. (It Makes Sense in Context - well, kind of.) Basically, he'll do anything to help his friends and he asks for absolutely nothing in return except their friendship.
Shamrock in Ace Combat: The Equestrian War is a good-natured, friendly pegasus fighter who comes, along with Talisman, to aid ponies in war with the griffins. Though his true reason for doing so was to calm his conscience that bothered him since the death of his little sister, Morning Glow, during the Anean Continential War, it doesn't affect his attitude toward others. When he opens up before Fluttershy, he thanks her for trying to cheer him up and even calls her "an angel that became a pony".
Last Child of Krypton: Shinji and Kaworu both qualify, although Kaworu becomes rather... different when he transforms into Black Adam, and in the rewrite he is very creepy and not nice at all. Regardless, Shinji is the nicest, most compassionate, most considerate and less judgmental person Asuka and Misato have known... par for the course when you are Superman.
Turnabout Storm has Lenora, a griffon racer and mail carrier. She's friendly, passionate about her work and hobby, and worried about her distressed friend; making an awful lot of contrast with the other griffon present in the series. Although she makes a point of not wanting to discuss anything regarding Ace Swift.
Shinji in Children of an Elder God is too nice and kind for his own good. He tries to be nice to and understanding with everyone, and he even tries to give Gendo the benefit of the doubt and think that maybe his father had a good reason for abandoning him.
ResurrectedMemories: Danny. He is ultimately a kind hearted individual who always uses his powers to do the right thing and he is extremely loyal to his friends and will not hesitate to protect them. It's these traits that eventually make Ember become attracted to him, due to the fact that he genuinely cared for her human self as a friend.
The OC Christopher Morgan is also a Nice Guy who becomes Ember's bandmate and is even interested in Sam to boot.
In the Twice Upon An Age series, this is how Varric (the story's editor) views Victoria, the Lady Inquisitor. She's really a bit of an Iron Woobie, but she's such a gentle and compassionate person that it actually concerns him. He remarks in a letter to Bethany Hawke that "Shes a sweet kid; this world isnt kind to sweet kids. I worry about her." The Lord Inquisitor is also an extremely Nice Guy, but he's snarky and pragmatic enough that Varric knows he can take care of himself.
Shrinking Violet tendencies and her lack of self-esteem aside, Amanda is easily one of the nicest and sweetest characters in the whole series. The little girl couldn't make a selfish wish if she tried and always tries to think about how her actions could affect other people. This was pretty much what ends up endearing her to Norm and later Timmy.
Corrin Reacts: A large part of the cast, however the eponymous character, Benny and Kaze are standouts, with Corrin wanting to play The Matchmaker for Flora's happiness among other things, Benny constantly watching out for Beruka's well-being and Kaze's niceness stunning Felicia for a little.
Several characters in Some Semblance of Meaning: Lark and Damon stands out as the most obvious examples, but Kit also has a good heart to balance out his sharp tongue, and for a Career, Obsidian is a very nice guy, indeed. As for the girls, there's the obvious example of Vale, along with her little sister Laurel, among others.
Satsuki Matoi from Maim de Maim is easily one of the most nicest people in the whole story one can ever hope to meet. Adding to this, she's quite forgiving and pacifistic towards her enemies, along with making new friends pretty quickly. Compare that to Satsuki in canon.
Takihara Fenshani from Seduction. He's helpful, considerate, doesn't hide what he feels, and nice enough to ask Sarakshi if he can kiss her before leaning in (not that the kiss ever happens, given Tora's interference).
Despite being called a coltcuddlin' pedophile, Caramel of Assumptions is as close to this trope as possible. He lets Rainbow Dash sleep on his bed while he gets the floor, after she accidentally drinks a spiked beverage. Then he cooks breakfast for her when she wakes, up, and again for over a month afterwards when she shows up expecting more. And even after it's revealed she nearly accidentally killed him with a botched stunt, Caramel chooses to accept her half-hearted apology so they could keep being friends. That's probably why she's slowly falling in love with him.
John from The Diary of John is really very nice, if a bit of a bore. Not once so far has he done anything remotely jerk-like. In fact, when he encounters a real jerk, one who's doing illegal things and bullying his friends, what does he do? Does he yell? Physically fight her? Drive her out of town? Turn his nose up and ignore her? Nope. What he DOES do is call the hospital when she (supposedly) gets hurt, comfort a friend whom she picked on, and informs the authorities of the illegal aspects of the whole business. All without even casting a nasty look at the bully.
Advice and Trust: Shinji always tries to be kind and polite. He even felt guilty after turning Chihiro down, because he thought maybe he'd been too harsh.
Evangelion 303: Kaworu is known for not having grievances, and he is nice, kind and understanding to the extreme. You have to work real, real hard to get him angry (not even Asuka manages getting him angry). And even then his reaction is feeling mild annoyance or disdain, and maybe avoiding you.
Ghosts of Evangelion: Shinji really tries to be nice to everyone and make things right after his mistakes led to the end of the world.
HERZ: Despite of some serious failings and bad actions which he regrets (such like his actions in the hospital when Asuka was comatose), Shinji is not a bad guy, and he genuinely wants and try to be a good person.
In Once More with Feeling Shinji tries to be kind to everyone. Asuka, Misato, Hikari... wonder why he's so nice, selfless and obsessed with making everyone happy.
Shinji from The Second Try thinks of himself as a throwaway, pathetic human being whose weakness and inability to deal with people and loneliness led to the extinction of humanity. According his wife, hes one of the kindest, most compassionate persons shes ever known.
He often said he was just selfish, wanting everyone to like him, and that's what she had thought for a long while herself. But compared with others, including herself, he was, even with that motive in mind, the most caring and compassionate person she knew.
Played with in The Keys Stand Alone: The Soft World. Whereas the four are Actual Pacifists and fiercely cling to that stance despite the semi-war raging around them, and they're not depraved or anything, they aren't portrayed as Nice Guys—even Ringo, who, despite having that reputation in Real Life, in the book is having major addiction problems that screw with his overall Nice-Guyness. However, compared to everyone else there, they come off as the Nice Guys, particularly Paul, who takes care to be polite to everyone who isn't actually attacking him. (It must be noted, however, that underneath the veneer of politeness Paul is often seething with anger or jealousy and needs his background noise to keep himself on an even keel.)
Ultimate Sleepwalker: Rick Sheridan was a pleasant but fairly unassuming college student when the alien Sleepwalker became trapped in his mind. He was more than a little pissed off about it when it happened, and fell into a downwards spiral after it happened, becoming isolated from his friends in the process...but he always let Sleepwalker out when it was necessary, willingly went back into the Mindscape with Sleepwalker so they could confront Cobweb, and when his friends began suffering problems of their own from their own tragedies, Rick proved to be the rock of the group and helped them cope with what they were going through.
Ser Addam Marbrand from the Continuation FicThe North Remembers, a close companion and brother-in-arms to Jaime Lannister. He's chivalrous, courteous, and hardly loses his temper even when things don't go as planned. He's one of the few people who recognizes the impending winter and invasion of the Others as a legitimate threat to the Seven Kingdoms, and makes the decision to turn the Lannister fleet against House Bolton because of their universally despised control over the North. While he forces Edmure to help him search for Jeyne Westerling because of the possibility of her carrying Robb's child, he doesn't do it so that he can kill the child himself, maintaining the Boltons' control over the north, but so that she could be returned to her family and raise the child themselves and possibly use it to bring the North back into genuine peace. When he does meet up with her, he doesn't even seem to care at all about the baby's crippled condition, and stands up for her when she receives a cold reception amongst the Northmen at White Harbour, assuring Jeyne that her son will grow up to become a good lad.
Hound is this in Transformers Meta. He has shown that his tolerance for Grimlock is higher than the other adult Autobots. However, that's not to say that the two don't have their bouts, like one having dirt thrown in his optics and the other getting slammed into a rock. Guess which one is which.
In Laura's Journal: My Story as Told by Me has Case Lancaster, Laura's love interest and the long-lost son of Victor Creed, aka Sabertooth. Despite Laura's occasional Designated Hero tendencies, he stands by her loyally, is willing to face down Logan because he likes her, and his niceness is actually enough to push Victor Creed of all people into a HeelFace Turn. He borders on being a Gary Stu because of this, but somehow he does it without it becoming too obvious.
Jimmy Frost, one of ZPD's new recruits in Born to Be Wilde, is a young arctic fox who's nothing but cheerful, educated and honest, traits that go entirely against the stereotype of his species and marks him as a foil to Nick. That's because he grew in a stable and supportive well-off family, and never had his innocence traumatically marred like Nick with the Junior Ranger Scouts.
Aside from her brief faux pas in the first chapter, Pandora might very well be the nicest character in the whole Pack Street series. She's never anything but kind, polite, helpful and generous to everyone she comes across, and is possibly the only person Remmy enjoys hanging out with without any reservations.