The Conscience describes a character type whose purpose is to act as the hero's (or other characters') conscience and moral touchstone, the person they consult to check that they're doing the right thing. Common when The Hero doesn't trust his own moral judgment.
Unlike The Heart, the role of the Conscience is not necessarily all emotion, and this role is thus available to a wider set of character types. In some settings, this character may be deeply religious and perhaps even a priest or preacher (of whatever religious system The Protagonist respects). His moral judgment is unlikely to be wrong, and is ignored at great peril.
Compare Morality Chain, where a character is kept on the straight and narrow against what would otherwise be his nature. Often one of the roles of The Consigliere.
Truth in Television, or so one would hope.
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Anime and Manga
Non-Kira Light, in a stark reversal, serves this function for L.
Noi the lizard in The Lucifer and Biscuit Hammer serves as an animal mentor and a conscience for Yuuhi. Noi is quite concerned about Yuuhi's desire to see the world destroyed.
In Digimon Adventure 02, Wormmon is the conscience to Ken, the Digimon emperor who badly mistreats his loyal companion.
Puck from Berserk tries to be this for Guts, calling him out on his less-than-heroic decisions and actions. Guts being Guts, however, he doesn't much care a lot of the time.
Riza Hawkeye crosses this with Morality Chain for Roy Mustang in Fullmetal Alchemist, along with being his bodyguard and personal assistant. Part of her explicitly-stated job description is to make sure he achieves his goals only through upright means - and to shoot him if he strays from what they have agreed is the righteous path. Since they are extremely close, she's not keen on the shooting thing (though she'll do it if she must), so when the time comes for her to keep that promise she does her level best to talk him down first.
Siegfried Kircheis serves as this for Reinhard von Lohengramm in Legend of Galactic Heroes, and continues to serve as one even after his death.
Kitty Pryde developed into this for the X-Men, doing her best to ensure the group's pro-mutant agenda doesn't take them into Well-Intentioned Extremist territory.
In the movie Necessary Roughness Scott Bakula's character (Paul Blake) abandons the team. When Jason Bateman's character joins him.
Paul Blake: You can't just walk away. Jarvis Edison: You did. Paul Blake: How did I end up with Jiminy Cricket?
In Ever After, Leonardo da Vinci might count as this for Prince Henry. He consults with him on important decisions and talks philosophically, looking to Leonardo to help guide him. And Leonardo's the one to call him out for the way he's acting near the end.
In the original book of Hammers Slammers stories by David Drake, Danny Pritchard ends up as Colonel Hammer's conscience, as Hammer's been too hardened by war to recognize when he's gone over the line.
In P.C. Hodgell's Chronicles of the Kencyrath, heroine Jame, who was raised among the Big Bad's minions, doesn't trust her own judgment as to right or wrong. During the first two books, Marc is the Conscience, her solid moral center; from halfway through book 3, Brier takes over the role, in a much sterner and harder-to-please way. Both of them inspire Jame's moral development.
Bunny Manders in E.W. Hornung's 'Raffles' stories. He always ends up helping in the burglaries, but never manages to do anything alone, and often prefers that they fail.
Cassie from Animorphs, though the others are not always willing to listen to her, and sometimes her ideas cause serious problems, like when she let Tom escape with the morphing cube to stop Jake from having to kill him.
Hermione in Harry Potter constantly reminds her two friends which school rule they're breaking in their latest plan. This diminishes over the course of the series until she's the one suggesting the rule-breaking activity.
Frankie Avalon's late 50s tune "Conscience" deals with a lothario who sets out to win young girls' hearts only to break them. That is until his conscience butts in and tries to dissuade him.
Live Action TV
Angel: Cordelia after she received the visions. She made sure Angel kept his focus on 'helping the helpless' rather than vengeance or making money.
Buffy the Vampire Slayer: Tara fits this role, especially in season 6. When Willow disregards Tara's advice, things tend to get... bad. She also plays this role towards Buffy, to some degree. Rather than being Christian, like most examples of this, Tara's a (spiritual, in contrast to Willow, who sees her magic as more of a tool) Wiccan.
Doctor Who: According to Donna this is why the Doctor needs human companions, so they can stop him. Needless to say she's right: While traveling alone the Doctor ends up risking the future of human space exploration by saving a woman destined to die in order to inspire those that make it happen. The woman in question ends up committing suicide to save the future in defiance to what the Doctor has become.
Firefly: Shepherd Book is a Good Shepherd trying to steer the Serenity out of the darker shade of grey. Wash too and ooften but Book's vocation makes one expect it more.
Revolution: You can almost see Charlie dancing on Miles' shoulder, telling him to be a good boy, as shown in the episodes "Chained Heat" and "The Love Boat". Funny enough, Miles seems to act as this to her at some points, as shown in the episode "Sex and Drugs".
Stargate SG-1: Daniel Jackson is the one talking about civilians and minimizing collateral damage and "think of the anthropological value of this site!"
Stargate Universe: Eli and Lt. Scott try to be this, though they are pretty ineffective.
Although Hobbes will often accompany Calvin in his mischief, he serves as Calvin's moral compass on a many occasion. He tries, anyway.
Bill McDonagh has been described by the developers as acting as Ryan's conscience in BioShock. The player arguably has Tenenbaum and Atlas who advise the player, Tenenbaum especially on issues like Little Sisters. Except they are both completely different characters.
The Player Character is this to Bastila, if they can convince her to turn back to the light in the end.
Digger acts as the newborn Shadowchild's conscience and helps it develop one of its own. This is very difficult since a) it's a sort of demon and b) it has absolutely no reference point for "good" or "bad" and c) they live in a world where things like Carnivore Confusion can be a really big problem.
And it looks like recent events have shown Digger did a good job. Of course, she needs a hug, now...
In Gargoyles, there is an episode with a golem. The role of one of the characters in that episode is to guide the golem's actions and help it stay in the right.
In the DCAUJustice League it was Initially Superman but it soon became The Flash. This is a plot point in the Cadmus storyline where it strongly implies that if Flash dies (particularly if he dies at Lex Luthor's hands), Superman will go crazy and kill Lex with his heat vision in a Roaring Rampage of Revenge. When the moment comes where Superman believes that Lex has killed Flash, he comes very close to doing it, but in the end relents and says "I'm not the man who kills Lex Luthor. Right now I wish to God that I was, but I'm not." Luckily, Flash turns out to be alive after all.
Kyle is often the one placed in this unenviable role in South Park as he's often stuck playing the voice of reason as well as the conscience in a show featuring Eric Cartman. While he can at times be a bit of a Jerk with a Heart of Gold at times, he's usually the one trying to do the right thing.
In "Fantastic Easter Special", Pope Benedict is this to Bill Donohue. "It's not very Christian."
Private of The Penguins of Madagascar is primarily The Heart, but assumes this role whenever Skipper and/or the others end up going too far. Though usually holding the moral high ground, he also tends to be rather timid when first voicing his concerns, gradually losing his patience as Hilarity Ensues.
Maurice is the conscience to King Julien. Of course, his advice always goes unheeded.