Male leads who good are looking, popular, and nice guys are as common in Shoujo as their female counterparts are in Shonen; wish-fulfillment is large part of fiction after all.
Jinto from Crest of the Stars, almost to the point of self-effacement. He's also Iron Woobie and The Quisling at the same time and thus makes an interesting protagonist despite having a less flashy personality than some of the other characters.
Takato Matsuki from Digimon Tamers. He's just a normal boy who is a fan of Digimon, as opposed to the rest of the cast which seems to have lots of Emotional Issues. This, of course, gets deconstructed.
Also Gabumon from the first season is easily the most gentle and polite of all the Digimon partners. He even took off his fur to warm Matt when Matt had a cold.
Spain, Canada, Finland, Thailand and Greece are the closest to the trope in between the cast.
Lithuania and Liechtenstein might count as well, at least in the main plot.
And according to the last manga volume, Macau is one as well:
His nature is rather ungreedy; he appears calm and good at business, is tall, and tries to be philosophical (...) He often has a businesslike manner, but he jokes around with Portugal, China, and Hong Kong. He treats Taiwan like a Proper Lady.''
Belgium seems to be one. She's very sweet and works hard, especially when her brothers are concerned, but doesn't really stand out much.
Along with Mai's brother Takumi, Kazuya Kurauchi is one of the genuinely nicer members of Mai-HiME's male cast, shown as a diligent worker and concerned with his girlfriend Akane's safety. He doesn't get much screen time, though, as he's the first one to get killed.
Hirasawa Yui of K-On is the idealistic, innocent and warm heart that holds the "Afterschool Teatime" band together.
Mikage of 07-Ghost. Complete with dying to motivate their hero buddy.
Bakuman。: They're everywhere. Which is natural, considering that it's a romantic comedy about writing manga. By the same people who brought you Death Note. The only real Jerk Asses in the series can be brought down to two: Ishizawa, who's had all of four appearances in this manga's over one hundred-chapter run, which, as of November 2012, is still going strong with it's third anime season, mind you, and one character who can't be named for spoiler reasons. It's also important to note exactly where the author choses to do this rather than creating a Jerk Ass character: the main editor had a lot of potential to be arrogant and dislikable, but they chose to make him a Reasonable Authority Figure instead; the main duo's rival, Teen Genius manga-writer Nizuma Eiji, also could have easily been an arrogant douchebag who flaunts his talent and power in the main character's faces, but he instead acknowledges their skills, thoroughly enjoys their work, often gives them helpful advice, shows up with a gift basket when The Hero is hospitalized, and wound up being voted the most popular character in a manga notable for its Loads and Loads of Characters.
Ayato from RahXephon is polite, friendly, easygoing and a decent human being. Amazingly, despite being the protagonist, he still manages to be a fascinating character.
Rock Lee. So much so that he forgave Gaara for nearly crippling him for life and ending his career as a shinobi. He's such a nice guy even Kishimoto admits he needs no Character Development.
Chouji Akimichi is another example. He's a huge softie, getting emotional when he has to fight his reanimated sensei, and both his father and sensei state that his kind nature is his greatest quality.
Hinata, of course since she did forgive Neji after he tried to kill her.
Naruto Uzumaki himself. His kindness and Not So Different properties have redeemed psychopaths, unrepentant killers, as well as starting to affect the Kyuubi. After he saves Konoha from Pain, it appears the village finally sees these qualities.
Of course, early Naruto was more a Jerk with a Heart of Gold - a foolhardly braggart who couldn't really understand how the people around him would feel about some of his behaviour, and sometimes made things worse because of his stupidity or boastfulness. It's after he mellows out - following the Time Skip - that Naruto really shows just how compassionate and forgiving he really is, though even in those early days he shows shades of this trope. Ever since he defeated and made peace with his Enemy Without, though, he's moved somewhat closer to being an All-Loving Hero, to boot.
There's also Iruka Umino, Naruto's Big Brother Mentor. His occasionally explosive temper aside, he's a very pleasant person to be around, being the first person to relate to Naruto on a personal level and never saw him as the Kyuubi unlike most villagers (notable because Iruka's parents were killed by the demon). Iruka's also an example of this trope done right - these very qualities are what make him an Ensemble Dark Horse, rather than the other way around (as the case would normally be).
And before all of these, Minato Namikaze (aka Fourth Hokage); even his future wife thought (at first) that he was a sissy because of his nice and polite demeanor. Like Father, Like Son it would seem.
And even earlier we have the First Hokage, Hashirama Senju. He is perfectly friendly and courteous to Sasuke, who at the time is trying to destroy his village and all he ever worked for.
Tenma in Monster couldn't be nicer, unless you happened to have dumped him for politico-economic reasons. And, even then, he'll still risk his life to save yours. Even after all the stalking.
Nice Guy-dom is used as a cover for at least two characters in Darker Than Black: Hei and Nick. In both cases, it can be hard to tell how much of the act really is an act sometimes.
Allen Walker from D.Gray-Man is as nice as they come (outside of a game of poker), not to mention absolutely adorable and prone to trying to save everyone. He's got two or three girls in love with him, and one of them is the sworn enemy of his species.
Ash Ketchum. He's pretty much the nicest and sweetest character in that anime.
Tracey, who replaced Brock for one half-season, is the embodiment of this trope. He's so polite and mild-mannered that many viewers write him off as bland and uninteresting. He Lampshades it in one side episode—after being pressured by Misty's oldest sister to clean the Gym, he's seen with a push broom and a sad expression, saying "Sometimes it doesn't pay to be the nice guy." (Just don't insult Professor Oak in front of him.)
Brock is no slouch, either. As Team Mom, he cooks and cares for his younger friends, provides help and encouragement with endless good-natured patience, and rarely loses his temper (when pretty girls aren't involved).
And then there's Luke who is one of the nicest of Ash's rivals/friends who doesn't insult him. His nice guy attitude is how he's able to put up with Bianca's quirks but even hehas his limits.
We have Nao from the Liar Game, perhaps the most pure and honest character in the whole series. In fact, her reason for continuing with the game is to save everyone else in the game, including the ones who had deceived and gloated cruelly in her face.
Kaworu in 3.0, to the point where one might believe he's skillfully manipulating Shinji. He's not.
Taichii Hiraga Keaton is an all around nice guy who happens to be a former sergeant in the British Army and a veteran of the Falkland Wars. Now he's an adjunct archaeology professor who also works as an investigator for Lloyds of London. Keaton is free from all of the arrogance and eccentricities that are normally associated with very smart people. Frankly, Keaton tends to meet all sorts of eccentrics in his line of work. Although he can kick ass if he wanted to, he prefers to use his intellect. So he's also a pacifist.
Suzaku Kururugi starts off looking like this, but there are hints that something is up (such as his childhood best friend Lelouch musing on the fact that he used to be brash, hot-headed, and arrogant, making Lelouch wonder what could change someone so much in seven years). Later on, we learn that he's not quite as nice as he seemed in the first place, but horrifyingly broken.
Meanwhile, Shirley Fenette and Euphemia li Britannia are the epitome of this trope when it comes to females. Unfortunately, this just shows us how the writers feel about Nice Gals in the cast.
Rivalz has shades of it, being a kindhearted slacker, and Gino Weinberg also has shades of it, as much as his duty as a Knight of Rounds allows.
Nunnally Lamperouge. She stays cheerful and kind through experiences that would leave most people shattered and is fortunate enough to survive unlike the above girls, albeit after some serious breaking.
Max Sterling/Max Jenius of Robotech/Macross is an unusual example of a definite Nice Guy who is also The Ace. And he's not the main character, either. (He does, however, get Happily Married half-way through the series, which the main character doesn't even accomplish before the series ends.)
Yuji of Shakugan no Shana is an interesting variation of this whose niceness actually does get him girls. Ironically, instead of stifling romantic conflict, his niceness is also his greatest flaw, actually creating romantic conflict in the first half of Season 2, where he completely fails to realize that he can't give attention to every girl who's attracted to him without hurting the feelings of someone else, thus making him an accidental Master of the Mixed Message. And his friend Hayato does call him out on that. Eventually, he becomes less so through the course of the series and averts it after merging with the Snake of the Festival.
Judai Yuki in Yu-Gi-Oh! GX probably qualifies too. In one episode, he accepts a challenge from an Obelisk snob with a wager, where the winner gets to be Asuka's fiancee - despite the fact that he honestly doesn't know what a fiancee is. (Unfortunately, Judai also has a Super-Powered Evil Side that causes him no end of problems later, and once he recovers from it, not everyone is pleased with the fact that he seems to be much more serious from the experience.)
Eiichirou of the manga Baby Steps. This is one of the reasons that Love Interest Natsu trusts him with her "big secret" (of wanting to someday become a professional tennis player) on the first day they met.
Eiichirou: Why did you let me in on your secret?
Natsu: ... because it's you. I mean, I know you wouldn't tell anyone.
Maison Ikkoku features Yusaku Godai, an honest example of this type of character. The series does not shy away from the flaws in these types of people — mediocrity/lack of ambition (or killer instinct), spinelessness (unwilling to hurt others' feelings), and being really indecisive. He also isn't entirely perfect, but he puts up with a lot of crap from others. And yet, his innate kindness and decency, along with his willingness to grow, more than compensate in the long run.
Ayumu Nishizawa is clearly a nice gal, paired with the fact that she's a normal person in a world where most of the rest of the cast are Ojous really makes Hata have to work to keep her relevant, and he does.
Hayate himself is a nice guy in general, despite being a Butt Monkey. Isumi is this as well.
Akira Sakamoto of Princess Princess is such a Nice Guy that his excess niceness leaks out and forms an aura of soothing and healing vibes that refreshes everyone who comes into contact with him.
Hayato Kazami is a very polite boy for most of the time, and is willing to make friends with just about anyone.
Johji Ohtomo. In fact, it's this very trait that makes him friends with Hayato.
Despite being a quiet person (at least in the third OVA), Phill Fritz from SAGA and SIN is actually a pretty nice guy. It's just that Nagumo doesn't want him to have any contact with anyone outside his team.
Makoto Katagiri, if we check on minor characters. He is the most well-balanced staff member of the Aoi team.
Tsubasa Ohzora from Captain Tsubasa; when he's not on the field, that is. Taro Misaki, Gino Fernandez, Luciano Leo and Pepe are also nice guys as well.
Even when in the field, Tsubasa is pretty nice. In fact, he's been injured more than once while helping a teammate or a rival, like when he saved one of the Tachibana twins from falling head-on first to the ground (which would've almost surely killed him, or at least caused horrible damage) and got a dislocated shoulder for his trouble.
There aren't a lot of nice people in this series, let alone nice guys. So you can guess why Judeau has become the resident Ensemble Darkhorse because of his nice, laid-back personality.
Later, Sixth Ranger Roderick has revealed himself to be a nice guy, though not as popular as Judeau.
Jerome from the Retribution Arc can pretty much be considered a nice guy as well, as he is far more decent than some of the other guys around him.
GE-GoodEnding features Utsumi Seiji, who is a pretty much an Unlucky Everydude who is sincerely nice to all his friends. Unfortunately, it tends to bite him in the ass as he sometimes ends up grabbing the Idiot Ball because he doesn't want to hurt anyone's feelings.
Kazuya Aoi from Freezing is the only one willing to look past Satellizer's shady background and discover that she's actually a really sweet girl, she just has some issues.
Dekisugi from Doraemon is this because his character is based on a perfect archetype of a Japanese schoolboy, in contrast of Nobita, who's a bit of a brat. In the movies, however, Nobita is upgraded into this trope, if not outright All-Loving Hero.
Dragon Ball sports a cast of various Nice Guys and Dogged Nice Guys among the heroes but Goku is one of the most famous in anime. So much so that nice guys of other Shōnen series have been based on him and his cheerful nature. No matter how grim a situation looks, Goku is always optimistic and smiling. He even dies smiling twice! He also easily forgives any villain that tried to kill him and his friends 5 minutes ago if they are willing to to stop being evil.
Yugo Hachiken from Silver Spoon is one of these, willing to do anything for his new found friends at the Yezo Agricultural School, and is also rather friendly. His classmates are perfectly willing to use him for menial labor for this reason.
Despite being a moron, and sustaining physical abuse from his friends, Akihisa is generally a nice guy, and even HELPS the same friends who hurt him on a daily basis when they are in need.
A number of characters in Fruits Basket fit this. Tohru Honda is the most prominent, constantly putting the wellbeing of her friends and family before herself, often causing problems for herself in the process.
Madoka from Rinne no Lagrange pilots a mecha because her friend she just made, asked her to.
Both Belldandy and Keiichi of Ah! My Goddess are nice people, each being the Trope Codifier for Yamato Nadeshiko and Nice Guy respectively. In fact, their relationship exists because Keiichi was a fundamentally good enough person to attactact a goddess's attention. Keiichi isn't a doormat; he's got a snarky personality and a backbone.
Nossori, Morimori and Sewashi from Mazinger Z, the three professors worked in the Photon Atomic Energy Research Institute by assisting Prof. Yumi and designing upgrades for Mazinger-Z and Aphrodite A were genuinely nice: they were kind, good-natured and very patient (you have to be to deal with so many hot-headed, impatient teenagers), even if they were somewhat goofy.
Sho Fukamachi in all three versions of Guyver — Guyver:Out of Control (1986),Guyver:Bio-Booster Armor (1989), and Guyver: The Bio Booster Armor (2005).
Tamaki in Ouran High School Host Club. His vices mostly come down to being an idiot, and a bit of a Drama Queen, but his all around niceness is the entire reason the club exists in the first place. He's the first person the twins met who actually cared which one was which, he calmly and quietly helped Haruhi when she was being bullied, and when he gave that bully what was coming to her, he still did so with politeness and grace. He's the top earner in the club, and as time goes on it becomes quite clear that it's because he's the only one there who is not acting to some degree or other and is in fact completely sincere. And that's not even going into how he deals with his Big Screwed-Up Family.
Nanami Momozono from Kamisama Kiss is the nicest, friendliest person in the entire series and is incredibly optimistic even when things look to be at their worst.
Takehiko Yoichi from Haiyore! Nyarko-san wears the term "nice guy" like a glove. Being a minor character he doesn't get much screentime, but he's cool enough to pass off Nyarko's madcap antics as merely being "energetic", and at one point remarks "My best friend has a cute girlfriend, and that makes me as happy as if it had happened to me." About the biggest thing that's happened to him so far is temporarily having his body hijacked by a time-traveling alien extremist.
Hasta as well. Cute, sweet, cuddly and good-hearted young boy. So much so that of all the characters in Mahiro's harem that consist of Cthulhu Mythos, he's the only person who didn't receive the wrong end of the fork from Mahiro.
Karen is a very energetic and friendly half-British, half-Japanese girl and can get along with her fellow classmates to the point that they give her free snacks.
Alice is such a kindhearted sweetheart loli. She rarely hold any negative grudges and feelings towards anyone. In episode 7, Alice even help improve and teach Shinobu some English language skills (which Shinobu will later get a good grade in the following English test) and even help cheer Shinobu up when Alice finds out that Shinobu didn't do that well on her math test.
Shinobu herself is a relatively friendly girl despite being the resident ditz (particularly when both Alice and Shinobu first met in episode 1)
This trope is lampshaded on Youko in Karen's pie chart as "50% comedic retorts, 50% kind-hearted."
Marco, one of two resident Team Dads, is genial, friendly, and always the one attempting to keep the peace and raise morale among his fellow trainees.
Petra, who takes it upon herself to act as Eren's Cool Big Sis once the Survey Corps gets hold of him. The guidebook even gives her a rating of 10/10 in Kindness, and it shows. Neither she nor Marco survive.