"Me, I'm dishonest. And a dishonest man you can always trust to be dishonest. Honestly. It's the honest ones you want to watch out for, because you can never predict when they're going to do something incredibly...stupid."
Matsuda from Death Note. He's honest and idealistic to a fault, and more often than not makes a nuisance of himself. However, his attempt to infiltrate the Yotsuba Group provides vital information, even though it backfires, and when Light Yagami reveals himself as Kira and starts gloating, Matsuda is the first to whip out his gun and start shooting. This is, incidentally, something like the true inverse of Bad Guys Do the Dirty Work—the closest surviving thing to a good person does the shooting.
And Euphie, ultimately, but it's not her fault! This world was made for Magnificent Bastards. To break themselves against, like Cuchulain fighting the sea, but at least they have a shot.
Mao, as well, tries to be as honest as possible, and he can see through anyone's lies because he can read minds; but he's a very dangerous villain.
Tenma from Monster is deemed untrustworthy by his director for choosing to operate on the patient who came first, as opposed to the patient off of whom he'd profit more.
Nao Kanzaki starts the Liar Game described accurately as "Foolishly Honest," meaning she expects everyone else to be just as honest as she is by nature. As the Game progresses however, Nao begins to prove herself perfectly capable of deception, and manages several Crowning Moments of Awesome through it. In fact, her lies have frequently relied on people being aware of her honest nature, since no one stops to think she might be lying.
Tamiya attempts to wrest back control of the Litchi Hikari Club from Zeera once the group approaches the Moral Event Horizon. Very fittingly, his epithet is "Bullet of Truth" and he is often shown as the most obviously upstanding member of the nine.
Jack Sparrow hangs a lampshade on this in the first Pirates of the Caribbean movie. In the third movie, he pulls it off himself: Pirates can only be counted on to be greedy bastards, which is why there hasn't been a Pirate King in a while (the position is democratically-elected, and they all vote for themselves). So when the vote comes up, Jack surprises everyone by voting for Elizabeth, making her win with two votes. He is definitely not an example himself, as he lies constantly and even the page quote is him being dishonest about his dishonesty.
It comes back to bite him when she trades him for Will. When Barbosa objects because Jack is a Pirate Lord, she simply responds, "King."
In Audrey, Wait!, the protagonist uses her national, live TV interview as a chance to spill the beans on everything leading up to this point, thus dispelling the gossip and rumours surrounding her (and helping out her friend Evan in the process by exposing their duplicitous label - on live television).
Several of Honor's own rivals have been left aghast at her willingness to drag some odious maneuver of theirs out into the open, when they had assumed that she would "play the game" the same way they would. It helps that her very refusal means they have no ammo for doing the same to her.
In Dan Abnett's Gaunt's Ghosts novel Necropolis, Sturm's attempt to make his plans without input from the other Imperial Guard officers is betrayed by Daur, who merely says, in his defense, that the officers had the appropriate security clearance.
Ben: Jacinta asked if her new skirt made her bum look big and Argent said, "Yes." Her teacher asked her if she'd done her homework and Argent said, "No." When she was asked why, Argent said her stepmother and father had a big fight about sex and she was too angry to write about diatoms for her Biology homework."
Penny: Oh, I see. Ouch.
Anaiya of the Blue Ajah in The Wheel of Time is described this way. Her lack of deceit continues to confuse the other plotters in the White Tower. Also, Cadsuane does this deliberately.
Galad is probably the best example in the series of this trope. His step-sister says of him, "He always does the right thing, no matter who it hurts." He is introduced to the main characters and the reader when he calls the guards to deal with a peasant boy (Rand) who has fallen over the wall of the royal palace and is being taken care of by the crown princess. She's apparently in no danger, and her brother is with them too, and no one wants Rand to be possibly thrown in jail over an innocent accident, but to Galad the rule about how to handle intruders doesn't allow for exceptions. Later, he joins the Whitecloaks on the strength of their ascetic philosophy, even though his mother and sister are members of or at least connected to the Aes Sedai, who the Whitecloaks all see as Satanic witches. Still later, when he suspects that his superior officer in the Whitecloaks killed his stepmother, he kills him.
Adviser Arfarra from Yulia Latynina's Wei Empire cycle might fit - while almost the entire Weian establishment is either corrupt or negligent, Arfarra is neither, but is instead a truly ruthless (but consistently, if not obviously idealistic) Knight Templar who has been described as being "capable of anything in matters that didn't affect his own interests" (as opposed to the character that described him thusly, who is capable of anything in matters that did).
Carrot from the Discworld Watch novels frequently triumphs because he is so honest and straightforward that the scheming, backstabbing people of Ankh-Morpork don't know how to deal with him. (Being strong enough to knock out a troll in a bar fight helps too...) Later on he acquires a good dose of cunning but maintains the image.
He's still scrupulously honest - in Men at Arms he's trying to get some information out of a Guild leader, and tells him, with a very serious air, that if the guildmaster doesn't do what he wants, he will, unfortunately and very much against his will, be forced to "carry out the order I was given just before entering." Said order? To leave quietly if the guildmaster refused to help. However, the guildmaster assumes it to be more along the lines of "break a few arms" and, in a panic, relents.
Cohen the Barbarian. Not because of his own honesty, but because he assumes everyone else is just as honest as he is. Thus in Interesting Times, when a soldier says, "I would rather die than betray my emperor", Cohen kills him. It doesn't take long for people to stop saying this unless they mean it.
From Harry Potter, Snape doesn't really lie to Harry. He hates him, his father, his untameable hair. He doesn't really lie to Dumbledore. He was a Death Eater because he wanted to be one. He doesn't dislike the cause. He detests Muggles and his lineage. It's nigh impossible to lie to Voldemort. He even told him he fancied Lily Potter, Voldemort just wouldn't hear of it. Fans spent years debating whether his attitude yet conflicting behavior meant he was on the good side, on the bad side or on his own, but he was never that much of a Magnificent Bastard and his goal was never that complex. He was just a Death Eater who made a Heel-Face Turn because he really loved Lily Potter.
Meursault in The Stranger. It never occurs to him to lie, even to save his own life. Why would his life need saving? Oh, because he's facing the death penalty for having shot a man. For no reason. Unless "the sun was bright" counts as a reason.
Subverted in the works of Ayn Rand where the characters who serve their self-interest are the idealistic ones. The untrustworthy villains are those who claim they want nothing for themselves, and will steal anything for the "common good".
In the Morgaine Cycle, Morgaine invokes this trope with her memorable statement, "With devils, there is dealing. Sometimes far easier than with an honest man." She has learned this by bitter experience.
Ned Stark from A Song of Ice and Fire. He puts Honor Before Reason and inadvertently furthers Petyr Baelish's plan purely because he insists on being honest and giving his treasonous opponents a fair chance. Indeed, it is precisely the fact that he puts Honor Before Reasonthat leads Baelish to regard him as expendable; he is too unpredictable and incapable of being negotiated with.
Live Action TV
Michael in Prison Break. Linc knows he is going to be executed but at least he has the satisfaction of knowing that Michael went to college and will have a good life. Except not because Michael cannot let Linc die for a crime he didn't commit so he gets himself sent to prison on purpose to rescue him.
Michael's idealism is a source of conflict throughout the show. It takes place in a Crapsack World so they should probably run far away but Michael wants to take down the company.
Star Trek: The Next Generation. Data doesn't lie. Supposedly ever. Which makes it all the more devastating when he does because nobody believes he can possibly be telling an untruth. An entire episode revolved around this concept with Data forced into lying by an order from his captain - who didn't know he'd made the order. It even helped him get away with attempted murder when he uses Exact Words to imply he had not fired a weapon intentionally just as they beamed him out ("perhaps something happened during transport")
Survivor. After Phillip got stuck on the wrong side of an alliance war, he was asked about what was going down. And promptly told the entire plan, despite his fellow alliance members trying to use him as a scapegoat. This distanced himself from the losing side, and proved his honesty, enough to sucessfully join in Boston Rob's alliance. It has to be seen to be believed, and was one hell of a way to start Redemption Island.
Played with a bit by Radical Honesty practitioner Eli Loker in Lie to Me. He's mostly harmless, just a little annoying.
However he veers into Honor Before Reason when he ensures a con artist is exposed and brought to justice, despite knowing that that this will mean the pensioners he stole from will not get their money back.
In Deus Ex: Human Revolution, David Sarif is an idealist who believes that augmentation can uplift humanity. He's willing to do shady things to fulfill this ideal like augmenting a comatose man above and beyond what was needed to save his life, circumventing the law to get information, compromise his own company's network to run secret background checks, and even frame an anti-augmentation organization for biological warfare based terrorism. Compare him with the other two guys Adam can help at the end of the game: Hugh Darrow, a guy willing to cause global chaos and mass murder out of a bitter jealousy of augmented people which he hides behind ostensibly noble reasons, and Taggart, an Illuminati stooge who is just trying to maintain the Illuminati's power over the world. The Illuminati initially wanted to recruit Sarif, but gave up when they realized that he was too idealistic to go along with their agenda.
Saxony Canterbury of Thunderstruck, who forms uneasy alliances with a Knight Templar organization willing to kill for sex in a chapel, a witch who killed his sister for a Human Sacrifice and Satan himself...all for the sake of two teenage girls.
The fact that Fighter is not a sociopath is often an obstacle the Light Warriors of 8-Bit Theater must overcome, such as here.
In Gunnerkrigg Court Jones warns Antimony about Coyote, stating that "Coyote is no liar, therein lies the danger."
The Reverend Darren England, in the Whateley Universe stories. He's so idealistic and so concerned about protecting the planet from demonic threats that he hires assassins to kill a schoolgirl, which leads to an invasion of the Superhero School Whateley Academy. On the other hand, the girl in question is prophesied to become The Kellith, whose spawn will wipe humans from the earth...
Interestingly enough, before the incident, she had already killed her own future self, theoretically negating that possibility. Also, if anything would make Kellith go evil, the stuff this guy does would.
However, considering his 'hate-filled sermons', he might just be a straight-out Knight Templar. Him helping to rescue Kerry in "Angel in Father John's Basement" helps, though.
In Transformers Prime, Dreadwing loses faith in the Decepticon cause and betrays Megatron by giving the Autobots the Forge of Solus Prime, giving them a fighting chance, when he realizes that Megatron doesn't really appreciate honor and loyalty.
In an episode of Gravity Falls, Grunkle Stan wears a set of magic dentures that force him to always tell the truth. Things quickly take a turn for the worst as Stan blurts out every truth that comes to his head.
The Business Plot, a reported conspiracy that intended to overthrow the American government in 1933 and install a fascist dictatorship, supposedly fell victim to this when the conspirators chose Marine Major General Smedley Darlington Butler to lead the coup. Butler instead chose to reveal the plot to the government, which fairly quickly brought an end to the conspiracy. You have to wonder how serious a plot it was to choose Butler since he had become famous for making radio addresses where he admitted he was ashamed of serving in the military and how it was used as a pro-business tool by the government. "Al Capone operated in three city wards. My Marines operated on three continents." He also was a socialist and had campaigned for the president he was expected to overthrow.
They probably picked him because he was the commanding officer of the force that was ordered to crack down on the Bonus Army, a group of impoverished WW1 veterans who were rendered homeless and jobless by the Great Depression, camped out on the national mall in Washington DC to request that the government pay them their support bonuses a bit earlier than initially agreed to, citing the hardship of the Great Depression as the reason they needed help more immediately. The particularly brutal crackdown against the bonus army was cited as a major factor sealing the fate of Herbert Hoover's reputation, but was part of what endeared Hoover to the conspirators of the Business Plot. They probably figured since Butler led that crackdown, he would be a natural choice for their plans. Fortunately for the nation, they figured wrongly.