Gantz: Masaru Kato. He is about as morally upstanding as they come, but he'll still pre-emptively ambush a guy on the toilet in order to defend himself and head off further violence.
Karakuridouji Ultimo: Sophia. He's on the Good Doji side, and is the embodiment of Wisdom.
Liar Game: Nao. Like Corporal Carrot, she started off extremely naive, honest and easily manipulated. As the game continued, however, we see that she is a lot smarter than she appears. She even schemes with Fukunaga and doesn't tell Akiyama and pulled it off, and often uses her innocent nature to trick and trap others.
Goku isn't even a complete moron. In Dragon Ball, he showed an unusual level of craftiness, and was shown to be at least reasonably clever. And that was outside of fighting. It seems he was just poorly educated.
Naruto: HinataHyuuga. She doesn't need to beat Neji in a fight, because her words alone revealed him for who he truly was during the Chuunin exams.
Fullmetal Alchemist: Ed and Al are child prodigies, and adapt to situations quite well.
Souten Kouro: Cao Cao is serious about upholding the law, but he's not Lawful Stupid and knows a set-up when he sees it during his tenure as police chief. As he said in exposing the eunuch Jian Shi's plot against him: "I am not the kind of fool that would kill His Highness, who you had caught in your wicked scheme!"
Comic Books
The original Captain America, Steve Rogers. Super-soldier, tactical genius, inspirational leader, unfailingly polite and incorruptibly idealistic.
...except when certain writers depict him as an idiot on the assumption that anyone that powerful must be Dumb Muscle.
It's because of his peerless strength that Superman is one of these by default. The only way to give him interesting stories is to give him opponents that work around his strength and test his wits. More often than not, Superman has to solve problems by highly specific and concentrated applications of force. In fact, he has as many if not more characteristics of a Guile Hero as an Action Hero, especially when faced with foes stronger than him.
It's implied that The Gentleman from Astro City is one of these. His goodness is never in question — he's unfailingly polite, selfless, and idealistic, even in the midst of battle. On the other hand, his intelligence to date has been largely implied; for example, he's one of the few super-beings who avoided capture during a secret alien invasion.
Spider-Man certainly has his flaws, he's hot headed, neurotic and can occasionally descend into bouts of self-pity, yet he's still extremely loyal to his loved ones, lives by a very strict Thou Shalt Not Kill code and above all else, he values responsibility. He also happens to be a genius scientist.
In Zatanna's ongoing series she is confronted by Oscar Hampel, who claims that he was turned into a puppet because of a tragic series of events almost out of his control and that his violent actions were an isolated event. Zatanna accepts that her father, for all his wisdom and power, was only human and might have overreacted by turning Oscar into a puppet. She gives Oscar the benefit of the doubt and agrees to help him become human again...after she runs him through a magic Lie Detector, that is. After all, just because her father was not perfect does not mean he was wrong this time, and she is going to make sure before she takes any actions.
Fan Fic
The dwarven noble protagonist in this Dragon Age fanfiction can be considered an embodiment of this trope.
The Reasonable Marines, a fanmade Space Marine Chapter for Warhammer 40,000, will attempt diplomacy first whenever possible, which makes then positively heretical in the shoot-first-ask-questions-never Imperium of Man. The fool that refuses their overtures gets to be on the receiving end of stealth tactics, combined arms and all-around Combat Pragmatism.
Film
Abbe Coulmier from Quills is a compassionate priest who believes Rousseau Was Right, and serves as a foil to the Marquis de Sade. While it initially seems like de Sade has the advantage, Coulmier turns out to be more than capable of zinging him right back, and punctures de Sade's pretensions to evil.
"You're not the anti-Christ. You're just a malcontent who knows how to spell."
Georgia Byrd from Last Holiday might seem naïve, but she is a very good saleswoman and gives some solid advice to other characters. Despite all of Kragen’s attempts to humiliate her, Georgia is usually one step ahead of him.
Batman is portrayed as such in The Dark Knight Saga. In fact, most of the plot of The Dark Knight revolves around the Joker trying to get Batman to break his moral code and prove that, deep down, everybody is just like him and that Batman's idealism is misplaced. He fails miserably.
In Cars 2, Mater's simple nature belies the fact that he's a genius at recognizing obscure car parts at a glance. He later uses this to identify Sir Miles Axelrod as the mastermind behind the efforts to sabotage the World Grand Prix.
Literature
Carrot Ironfoundersson greets everyone by name, is perpetually polite and cheerful, and selflessly volunteers to help anyone in need. But anyone who mistakes him for an easy mark quickly learns otherwise.
And that was Carrot at work. He could sound so innocent, so friendly, so... stupid, in a puppy-dog kind of way, and then he became this big block of steel and you walked right into it.
While Sam Vimes is a textbook example of Good Is Not Nice, his wife Sybil is an example of this trope. She's always unflappably polite and kind-hearted (even to Nobby Nobbs), but beneath her lighthearted exterior is a razor-sharp mind, as demonstrated when she negotiated Ankh-Morpork's fat trade with the Dwarf King in The Fifth Elephant.
And then there's Nanny Ogg, the Cool Old Lady who's always up for a good drink, a good smoke, and a good ribald song. Yet she's smart enough to keep Granny Weatherwax in check...
In The Hunger Games, Peeta is kind and patient and totally kills people in the arena, including finishing off one girl in cold blood while he's in the Career pack, besides being three steps ahead when it comes to manipulating the on-camera narrative.
The Father Brown series, by G. K. Chesterton, uses this heavily with its titular character. In his first appearance, the Gentleman Thief Flambeau is shocked that a quiet, unassuming priest can not only outwit him but knows more than him about criminal behaviour. Father Brown points out that of course priests know these things; people confess to them.
None of the main cast of Codex Alera can be considered dumb, but Tavi in particular stands out. He's constantly derided for being overly idealistic and trying to make peace with nonhuman species who have been at war with Alera for centuries. However, he's a Guile Hero with a talent for Crazy AwesomeBatman Gambits and understanding creatures that don't think like humans, so as often as not his idealism actually pays off, much to the surprise (and sometimes annoyance) of his detractors.
Jim Butcher's other series, The Dresden Files, also uses this trope on the Knights of the Cross, Michael Carpenter in particular. Michael is a Church MilitantKnight in Shining Armor and devout Catholic, but he's also a perceptive person. If it looks like he's falling for a plan, it's because he believes it's the only honorable way to get Harry out of the latest mess and/or God will see him through it, never because he hasn't noticed the risk.
Also because Harry has risked the same for him.
Brother Cadfael from the Ellis Peters mystery novels is a very intelligent man, quite good at medicine, reading people and bringing the most unnoticeable clues together. He is also remarkably kind and compassionate. Hugh Beringar is also a good and honorable person — and a Magnificent Bastard on top of that.
In Timothy Zahnnovels, Luke is written this way. While he may be one of the strongest Jedi, he is also able to outsmart his opponents when necessary.
In The Lord of the Rings, Frodo makes it very clear to Gollum that he is well aware that Gollum is trying to think of a way to betray the hobbits and take back the ring. Sam is surprised at this because he had assumed Frodo was far too good a person to be able to understand deception and treachery. Sam admits that he (and probably Gollum as well) "had confused kindness with blindness."
Live Action TV
Benton Fraser from Due South. Honest, noble, impeccably polite at all times... and a lot more competent and intelligent than he appears.
Incredibly reminiscent of Captain Carrot, to the point that you think somebody must have been inspired by somebody else. Apparently not, though.
Dr. Molly Clock in Scrubs. Her cheery optimism refuses to yield even against the naked cynicism of Dr. Cox and Dr. Kelso, and allows her to triumph against them.
Rodney McKay was quite surprised to find that Col. Sheppard has a Mensa-worthy IQ.
In the Firefly episode "Trash," Saffron assumes Mal is an idiot because he's being kind and compassionate to her. Then she walks headlong into his Batman Gambit when it turns out he expected her sudden but inevitable betrayal, and Inara beat Saffron to the drop point.
Carly in iCarly sees the best in people, but if betrayed or oppressed, will come up with a scheme like having a massive in-school riot to get the good principal back.
Occurs several times in Survivor — Natalie in Samoa successfully played Russell's scheming to her own benefit. Also "Fabio" in Nicaragua, who had a "lovable goof" personality but was reasonably game-savvy and combined the two to get the win.
On Season 2 of The Amazing Race, Tara & Wil and Chris & Alex constantly ragged on Blake for being an idiot, despite this, he made several brilliant strategic moves, including being the first team to beg for money, getting his bags on a flight when all the other teams had to check theirs, and getting preferred parking on a ferry, most of which were decried by the above teams as "cheating".
Part of Boston Rob getting Uchenna & Joyce and Gretchen & Meredith on a faster flight in Season 7 (when Rob, in order to mess with their heads, mentioned a fictional earlier flight, which just turned out to exist) was him talking about how Uchenna & Joyce couldn't do anything for themselves.
Eiji Hino from Kamen Rider OOO may seem like a carefree fool, however underneath his simple exterior lies a rather cunning mind.
Probably letting Elnora the mercenary go in Mass Effect 2.
Even that's understandable. Shepard didn't have the time or manpower to take a person prisoner even if s/he knew that she was a murderer. And Paragon Shepard is not someone who's just going to gun a defenseless person down.
Taken to the extreme in the Overlord DLC. At the end, when Shepard discovers what Dr. Archer did to his autistic brother David, s/he's reasonably pissed off, and tries to take David away to get treatment for the torture he's endured. When Dr. Archer brandishes a gun at Shepard, the player has the option to pistol whip him... as a paragon interrupt.
The renegade option, for the six billion of you who didn't take it, has Shepard leave David with his brother, but s\he still smacks him around and tells him he's a sick bastard who's only spared because the project might prevent a war.
Garlot of Blaze Union may not be very smart to begin with, but he has a very sensitive nature that allows him to accurately read and understand his rivals and enemies' motivations. As his adventures start to gain him more and more street cred, it's his overwhelmingly gentle and compassionate heart that manages to win the hearts of his entire country—including those very rivals and enemies, more often than not. We get to see in the future just how much Bronquia really appreciates having a leader who's kind, just, and competent.
Almost all of the good guys in The Order of the Stick fall under this trope, with the exception of Elan. Paladins even state outright (several times) that they're "Good, not dumb."
And even Elan isn't completely dumb, because what he lacks in book smarts, he makes up for in Genre Savvy.
Miko might be another exception. "Good, not dumb" is often a response to people expecting other paladins to act like her.
Miko, if anything, is a Deconstruction of Dumb Is Good as she's too stupid and stubborn to deal with complex moral situations.
Hell, even Miko can't be underestimated, because she managed to track down the Order across a continent, and possessed enough of a tactical mindset to defeat the Order twice with only her horse as backup and damage/kill most of the raiding ogres in the opening round of combat.
Arthur in Arthur, King of Time and Space. His enemies often assume that because he's nice, unassuming, and prepared to give the benefit of the doubt if possible, he can't be dangerous. Many of them are dead now, and the remaining ones still haven't learnt.
Everyone thinks that just because Gilgamesh Wulfenbach never built a Death Ray and tries to be civilized and fair, they can push him around and act like he's nothing. When he's finally pushed over the edge, he shows the entire world that yes, he does know how to build a Death Ray, and yes, he's perfectly capable of kicking the crap out of Europa to protect his father and not-girlfriend.
He doesn't build a Death Ray, he builds a device that can summon forth energy from the environment. LIKE LIGHTNING!
This is apparently accepted under Europa's cultural definition of 'death ray.'
When he does flip out and brings this up, he scares some very hard to scare people, while delivering an incredible beatdown to the oversized war criminal sent to retrieve him. And at the end:
Gil: Well, you know what? I can do crazy. I really can. And it looks like I'm going to have to. Agatha is in danger. This whole town is in danger. If I'm going to be able to help her at all, I'm going to have to give up all this "being reasonable" garbage and show you idiots what kind of madboy you're really dealing with! [Smashes Vole apparently through a wall, Beat, sudden wide eyes] ...oh. Oh, no. This must be how myfatherfeels - all the time!
Gil's probably just as much of a case of 'nice is not harmless,' though. You could even make a case for filing him under 'Good Is Not Nice,' especially lately, despite being an Overlord Jr.. The...three-year day...since the above incident has not been easy on him.
Western Animation
Arguably Ned Flanders from The Simpsons, at least in the early seasons. He's smart enough to outsmart Homer, though that's not saying much.
In the Justice League episode "Flash and Substance," Orion asks why Central City would honor a buffoon like the Flash, "who makes bad jokes, who concerns with pitiful men like the Trickster." But the Flash is anything but dumb—he's able to handle the Trickster without throwing a single punch. In fact, he convinces the Trickster to happily turn himself in to the police.
He's also a forensic scientist in his civilian job, and a good one too.
You can tell that even Batman is almost envious of his ability to quietly shut down a super-foe, something he cannot imagine being able to do in Gotham.
It does help that The Rogues are Punch Clock Villains rather than crazies Batman has to deal with.
Real Life
Studies show that more trusting people are often more capable of telling when others are lying.
Which is the kind of Fridge Brilliance only found in Real Life. A person gets mistrustful if they get burnt one time too many - if you can see lies and deceptions coming, people will not get a chance to betray you, and therefore you will not become hurt, wary and eventually (possibly) paranoid.
The opposite could just as easily be argued if one sees 'being lied to' as the cause and then 'becoming more apprensive of potential lies' as the effect, rather than the reverse.
A more likely explanation is simply that people who are more trusting of others are typically those with good social skills. Which makes them better at spotting and interpreting body language, getting a rough idea on other people's moods and current mental state (stressed, agitated, relaxed, bored, etc.) - and all of that helps in figuring out if someone is telling the truth or lying through his teeth.
It could also be the other way: if you can't tell when people are lying, protecting yourself means assuming that everyone might be. Being good at telling when people are lying means that you don't need that, so you can be trusting.
It's quite likely that all three explanations contribute to the effect. Psychology!
How about, if you lie to many times, the only ones who will hang around you are those whom nobody trusts?
