Masayuki in A Profile is so nice that it unnerves some of his friends and classmates.
Tsukihime's Tohno Shiki is a decent, compassionate guy. Don't fuck with him or he'll make you Deader Than Dead. Or for that matter, fuck him. Dude's a living aversion of Good People Have Good Sex. His niceness was most likely a result of a traumatic incident where he almost died so now he ended up appreciating life more.
Shiki is more of an average guy then a real nice guy. Sure he'll risk his neck to rid of a killer if he feels its within his power (or if he's force to) and he'll put on a smile for you but in truth, he don't really care all that much for some strangers. For example: When he first heard of the murders his thought process was: Must suck for the victims; oh well, nothing I can do, on with life. He also admits when helping Arcruied that that he's not really doing it to help the city, he's helping her because he wants to help her. Guess he's one of those "fake nice guys" the guy above was talking about; definitely a nice guy but not a saint.
On the other hand, regarding strangers, when he was facing Nrvnqsr Chaos, witnessing the latter interrupting their confrontation to murder and devour a bypasser who had nothing to do with anything, for no reason whatsoever, was what got him out of being afraid of the monster, and replaced the fear with hatred and anger.
On the female end Hisui is the only Heroine who doesn't actively do anything that endangers Shiki's health mental or otherwise jokes about her bad cooking aside.
In Lux-Pain, out of all of Atsuki's new friends, Ryo fits the definition and is well known for being the nicest guy at Kisaragi High School because he's so helpful. Of course, he's a character that you don't want to anger but his annoyance is always justified. And of course, his nice guy attitude is what attracts the ladies and his best friendHibiki. He's also the Team Dad of the group.
Yayoi is the nice girl of the group always worrying about everyone's safety and like Ryo, she's the Team Mom of the group.
George (who happens to be Hideyoshi and Eva's son) and Jessica can probably apply for this too. With the same, necessary caveat, of course. George to an almost ridiculous level, to where almost any sarcastic jab Battler or Jessica makes results in a scolding from him.
Hideyoshi is slowly becoming an Ensemble Dark Horse because of how normal and friendly he is. In fact, the fandom is displeased that he hasn't gotten much character development.
According to Episode 1, all he wanted was a family that would accept him because his died during World War II.
Makoto Naegi from the first Danganronpa visual novel falls into this. He's the most kindhearted character that he can get along with everyone, including Celes and Togami (who are very difficult to befriend). Even some of the most anti-social classmates can be befriended by him in free time events.
Sonia Nevermind from Super Dangan Ronpa 2. She's polite and charming and gets along well with everyone, and she doesn't have a mean bone in her body. Which is probably why she's one of the few students who survives the entire game; she provokes no one into killing her and she never has any desire to kill anyone so she isn't executed. Though it raises the question of how she, along with the rest of her classmates, fell into Enoshima's despair.
Akane in Nine Hours, Nine Persons, Nine Doors is a sweet Ill Girl who is very concerned for everyone's safety. Nope. That's all a front, and she's the one who set up the game, kidnapped all the players, and orchestrated the murders of three people. Being kidnapped and murdered nine years previously (and no, that's not a typo) by Ace turned her into quite the Magnificent Bastard.
Luna in Virtue's Last Reward is a sweet, pacifistic girl. It's not a trick, even though the game wants you to think so. In the AB game, she never chooses betray.