Even more so in the Ultimate universe, where he's one of the few unambiguously good characters and fights crime purely because it's the right thing to do.
Dick Grayson.DC Comics' official position is that he's the most beloved superhero in the community (yes, even moreso than Superman) and that almost any member of it would instantly drop what they were doing to help if he were in trouble.
Tim Drake, Robin III is also a nice guy, especially in his early Robin Series. He took care of his girlfriend who was pregnant with her ex-boyfriend's child, and is good at babysitting kids. In the new DCU, he was also called a nice guy by Wondergirl.
Scott Pilgrim from Scott Pilgrim is ultimately one. Scott is by no means perfect, being The Slacker, a bit slow and does not think things through resulting in him sometimes inadvertably hurting those close him. However, he is pretty amiable, is the least hostile out of his group of friends, and Ramona did call him the nicest guy she dated (granted, everyone except perhaps Lucas Lee were jerks of varying degrees.) Scott's friends tend to veer more toward Jerk with a Heart of Gold
Mr. Tawky Tawny in the Shazam franchise sometimes causes a scare for being a humanoid tiger, anyone who takes the time to know about him will realize that he is a perfect gentleman and a wonderful person to know.
Major Mapleleaf from Alpha Flight, as befits a super-Mountie.
Jaime Reyes' Blue Beetle is basically Spider-Man without the world crapping on him as much. Thankfully, he has (or had thanks to Flashpoint) a strong supporting cast he could play off of.
And of course, the Flash. No matter which one, The Flash will be this. Golden Age Jay Garrick, Silver Age Barry Allen, Bronze Age Wally West (though he bounced between this, Jerk with a Heart of Gold and Chivalrous Pervert), Dork Age Bart Allen, all of them are consistently great guys who can and will become the best friend and surrogate brother of anyone they're with.
Captain Marvel is this in most incarnations, despite a fairly rough childhood. Billy Batson is usually a really sweet guy, often remarked by other characters as being polite, friendly, kind and 'sunny'. And despite being able to turn into a superpowered demi-god, he is just as polite, friendly and kind as Captain Marvel. The Nu-52 version of Billy averts this, being a Jerk with a Heart of Gold , with said heart being buried waaaaay down beneath a whole lot of jerk.
Klara Prast of the Runaways. She's perhaps the only member of the team with absolutely no Deadpan Snarker traits, and is usually far less inclined towards violence than her teammates. Of course, as an immigrant from the early 1900s who was brought into the present, she can sometimes be an Innocent Bigot. Also, God help anyone who threatens her - her plant friends can get very protective...
Hollis Mason, in Watchmen, doubles as the Only Sane Man. He's humble, friendly, and took up his career because he wanted to be a superhero. About the only thing he did in the story that could even count as mean was calling out a few people in his autobiography, and even then, the only person who really got it was The Comedian.
In Fables, Boy Blue is possibly the nicest character in the series, being eternally friendly, polite, hard-working and caring. However, Beware the Nice Ones is in full effect; in his past he was a brave soldier, but he deliberately chose to be a boring office clerk because he simply didn't like adventure and fighting. When circumstances demand his return to action, however, he reminds everyone just what he can do, and even when he's not in action he's not afraid to call people out if they're behaving stupidly. The problems of the Nice Guy character in a romance arc actually get discussed in-story; Rose Red was definitely attracted to him after his adventures, but the attraction wanes when she realises he doesn't actually want to be an exciting person and was quite content to be an unpretentious nice guy, which didn't mesh well with her own preferences for danger and excitement.
The Frog Prince Ambrose is another example, though in a slightly different way; Ambrose at first gave off the Dumb Is Good vibe, while Blue's intelligence, courage and skill were known quite early on in the series, making his niceness more of a deliberate choice. However, it's later discovered that Ambrose takes it all the way up to Incorruptible Pure Pureness levels, and the Messianic Archetype powers he later gets are dependent on him maintaining this. He is best friends with Boy Blue, who points out that Ambrose was the only fable who had absolutely no crimes to be absolved of under the amnesty.
Mighty the Armadillo from Archie's Sonic the Hedgehog comic. Unlike most beings on Mobius, Mighty is so damn strong that nothing really poses a threat to him. Mighty uses this strength to benefit those that are weaker, including his less-brave friend Mighty the Squirrel and his long-lost sister Matilda. The only time that Mighty loses it is when he perceives harm as having come to his friends.