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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".
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.
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.
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 accidentaly drank a spike drink. 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.
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.
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 off 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 log lost son of Victor Creed, Sabertooth. Despite Laura's occasional Designated Hero tendecis, he stands by her loyally, is willing to face down Logan because he likes her, and his niceness was actually enough to push Victor Creed of all people into a Heel-Face Turn. e borders on being a Gary Stu because of this, but for some reason, he does it without it becoming too obvious.