Despite being a necromancer prone to being a Large Ham, Dr. Orpheus of The Venture Bros. is a loving father, true friend (to Brock Samson and his Triad team-mates at least) and one of the few characters on that show to have a conscience. Although he takes his share of hits and occasional ridicule (like every other character), he usually comes out on top earning at least the respect of his peers. He even states that he only uses the Necromancer label due to titles like Wizard or Sorcerer being too boring.
Which is ironic, considering his mentor and teacher is one of the most Jerk Assey characters in the entire show. He might not match the Monarch or Phantom Limb in terms of objective evil but he manages to outdo both in terms of sheer, petty passive-aggressive meanness. Somehow, Orpheus always manages to take his advice in a way that doesn't make him act like a total ponce, which only helps contribute to his Nice Guy cred.
Orpheus does become easily aggravated with the Outrider, who if anything is even more reasonable and polite than even Orpheus. Given that the Outrider married Orpheus' ex-wife, that's not exactly unusual, and they seemed to get over it by "The Better Man".
The rest of the Order of the Triad are unusually reasonable for the universe, as well : The Alchemist's worst aspect is a grudge against the Internet after finding out that a boyfriend was cheating on him through MySpace, while Jefferson Twilight gets a little frustrated that his skillsets are fairly specialized.
Revenge of the Island adds Mike (at least when his main personality is in control), Sam and Cameron, who, after he wins in the finale of said season, gives a share to every one of his friends and his enemies.
Mac from Foster's Home for Imaginary Friends. And Wilt who manages to dodge the "Butt Monkey" and "Not funny" aspects of this trope by being SO much of a doormat that it becomes hilarious. Part of his problem is a chronic inability to refuse any request, no matter how ill-advised acceding to it would be. In one episode he finally flips and shouts "NO!" over and over for almost a minute...before Bloo heartlessly makes yet another selfish request and force of habit elicits an amicable "sure!" from Wilt.
Phineas and Ferb: Jeremy Johnson is such a pleasant person, it's hard to believe he has an absolutely insane little sister. He's even dating Candace despite all her glaring flaws and questionable sanity.
For that matter, Phineas and Ferb themselves would give you the shirts off their backs if asked. In theory, at least. In practice, they'd be more likely to invent some kind of humongous shirt-making machine to clothe every shirtless person in the Tri-State Area, but the principle's the same.
Captain Marvel on Justice League Unlimited. He only got one episode, but managed to be a bigger Boy Scout than Superman.
Superman: Why are you— why is everyone defending him?!
Batman: We like him. He's... sunny.
And several minutes of Cap's episode were dedicated to showing how well Cap got along with his teammates and how nice a guy he was to them. This was done specifically to contrast the seven core JLU members, who during that season were shown to hang around only each other, have secret meetings with no input from the rest of the team and not really interact with the 'lesser' heroes. This gave more credence to the What the Hell, Hero? speech he gives the big seven, specifically Superman, at the end, regarding their behavior.
Butters from South Park. He has endured heaps and heaps of Break the Cutie that would have caused anyone else to jump out a very high window with a smile and a song. Even his parents are in on it; his mother tried to drown him in a car when she found out that her husband was sleeping with men, his parents grounded him for making a funny face (his normal face mind you) in his class photo, and they even tried to sell him to Paris Hilton when her latest pet committed suicide. Occasionally he will deliver harsh words, but only when people deserve much, much worse. He did decide to become a Super Villain, but even that is just plain precious.
The titular Doug is probably the sweetest kid in his town, always being there for his friends, rooting for the underdog, that's just a few things.
IM Weasel from I Am Weasel. Calling him nice would be an understatement. He was first shown giving a dying boy a kidney transplant. He becomes slightly more egotistical and neurotic in later episodes, though considering how much his kindness often gets him, it's often justified.
Mei Ling in the short Kung Fu Panda: Secrets of the Furious Five. She is the only one who realizes that Crane, who is working as the underappreciated janitor, not only dreams of joining her academy, but has the talent to excel. As such, she takes it upon herself to convince him to try out for enrollment and she backs him all the way in the attempt.
Ed the otter from Brandy & Mr. Whiskers is one of the nicest, most likable, most easygoing characters on the show.
Strangely enough, Stewie Griffin frequently plays this role in his interactions with Brian, despite being a complete sociopath elsewhere. Quagmire will sometimes adopt this role, especially when interacting with Lois and the younger Griffins, although he usually cycles back to his role as the pervert fairly quickly (Rule of Funny wouldn't you write him that way, too?). Joe and Brian are probably the closest the show has to your standard Nice Guy nowadays, particularly when interacting with the Griffins, although Joe is too aggressive and driven to fit the role exactly. Brian fitted this role well in the early seasons, but he's probably too self-righteous and disliked by the fanbase to really work as your standard issue Nice Guy.
Even with Brian, Stewie once gangster beat him, made an elaborate hoax to attempt to get him neutered and travelled in time to ruin every enjoyable moment in his life (the majority of these were largely just because he could). He does have kind moments with Brian, and puts up with a lot of his own selfish and abrasive behavior in return, but he's still a Jerk with a Heart of Gold at his very best.
Chris from Dan Vs., in stark contrast to Dan (and most of the other characters to be honest).
Fry from Futurama is incredibly stupid and ignorant, which makes him act crude, inappropriate, or thoughtless at times, but his disposition is always sweet and sunny and his intentions are always good. He's also incredibly selfless and forgiving, especially towards Leela and Bender.
Kim Possible may have traits of arrogance, vanity and has a slight habit of being bossy, but she mostly matures out of it to become genuinely more caring, tolerant and respectful. Mostly.
PJ is honest and ethical to the point where he sometimes forgets his Manipulative BastardAbusive Father isn't and is unwilling to break the letter of a promise to him (even if he breaks it in spirit), has Undying Loyalty towards Max even when Max treats him inconsiderately, is very patient and forgiving in regards to his mistreatment, intentional or otherwise most of the time, is a helpful, supportive friend, and manages to have genuine sympathy for people who are significantly better off than he is. The only things keeping him from being an All-Loving Hero are his world-weary attitude and occasional rudeness.
Goofy, who does cause some problems due to his clumsiness and stupidity, is also an extremely patient friend and a Good Father (sometimes to kids other than his own). All Goofy really wants to do is help other people out with their problems, and is willing to forgive a lot of things. He also hardly ever has a bad thing to say about anyone.
Roxanne from A Goofy Movie is a nice girl, as shown when after everyone laughs at Max for falling off the bleachers, and she's the one to show concern for him.
The eponymous character of Mr. Bogus would also fit this trope, as even in spite of the fact that he is a gremlin and just 3-4 inches tall, he is actually one of the nicest characters ever in most situations.
Tom Sloane from Daria. He, more or less had a hatedom and changed Daria's life in the final seasons, but still manages to be the most pleasant guy in the series. He's an incredibly reasonable person, who tries hard to get along with everyone even if they're hostile toward him.
As stated before Xander and Foxxy Love are the least-depraved people on Drawn Together. In particular, the former is eager to help most people, including his Abhorrent Admirer Toot Braunstein, while the later has her share of (mostly self-harming) flaws, but usually recognizes them, is ashamed, and makes at least some kind of attempt to correct them. Both are also very open-minded.
Wooldoor also leans towards this as, like Xander, he mostly wants nothing but to help people out. Unfortunately, this is severely punctuated by incredibly dark statements and behaviors on his part, though it's implied he isn't usually actively malicious and instead is less than sane.
Darwin from The Amazing World of Gumball. He becomes more aggressive from the second season onwards, but he still remains a Cheerful Child. When he was possessed by a spirit of jealousy, he reveals that "[he's] actually quite happy with [his] life" and holds no spite or envy towards anyone else.
Darwin: Is he gonna cry? Because if he cries, I'll cry!
Also Penny, who's one of the nicest characters in the show.