Used in Claymore whenever the characters need to go undercover.
The protagonist's disguise in Code Geass involves a helmet that completely hides the face and a black cloak. Though it remains a mystery if he really is a good person, or is just wanting power for himself.As of the series finale, he is officially a good guy - one might even call him "Christlike..." For obvious reasons.
In the manga series that's most faithful to the anime, Lelouch actually does wear a black cloak before having Zero's costume made.
Nekozawa from Ouran High School Host Club wears one of these partially to be mysterious, and because he is extremely photosensitive. He even wears a black wig over his normally blonde hair. Oddly for this trope he's not evil.
Naruto has the Akatsuki, who have painted very stylish red clouds on their Black Cloaks, which, in a minor subversion, don't come with hoods (though they do have conical straw hats).
Not to mention that the Akatsuki's robes apparently have speakers in them, as whenever they appear for the first time in an episode you hear a chorus intoning something that sounds like "DESHTOOOOOOOOOY, SEPHOIREEEEEEEEE..." Somehow, that just makes them even moreBadass.
You can tell when an Akatsuki is about to die, because they will generally throw off their cloak or it'll be burnt or destroyed.
And for the ones who have died, when Kabuchimaru revives them with Edo Tensei, he so very thoughtfully provides them all with hooded black cloaks, playing the trope dead on.
There's a recent couple of panels in the manga in which Sasuke and Madara/ Obito Uchiha are just sitting around in a tea house with no disguise other than a black robe. Seriously.
Exedore/Exsedol's redesigned form in the Macross universe: his entire body below the neck is shown as a black cloak with retractable tendril-like arms, but he's a fairly nice guy who serves as The Spock instead of being a villain.
Wiseman aka Death Phantom, Big Bad of the second season of Sailor Moon is a skeleton in a black cloak.
Shinigami from Soul Eater seems as if he's wearing one of these, though it's hard to tell if it's clothing or his actual body. When wearing his black robes and skull mask, Death the Kid looks like a miniature of his father (the first time it looked like it was until the perspective changed).
Almost all of the Dark Signers in Yu-Gi-Oh! 5Ds don black clocks. Those that do are typically shown hooded before they officially reveal themselves to the protagonists, ditching the hood for all subsequent appearances thereafter.
In his progression from innocent farmboy to Jedi Knight, Luke Skywalker started in a white outfit (A New Hope), underwent most of his training in a grey flight suit (The Empire Strikes Back) and wore a black jumpsuit under the traditional brown robe when he proclaimed himself a full Jedi Knight (Return of the Jedi). Also, at the end of RotJ, note that he comes to the celebration at the end with the front of his tunic partly unzipped... resulting in a patch of gray, surrounded by the dark. (The comics and novels that take place afterward state that he had stained himself with the Dark Side quite a bit by then, but they were primarily written after the fact and may be considered a Retcon.)
The Emperor/Senator Palpatine/Darth Sidious, who shows up this way in the original trilogy, the prequels, and the Animated Adaptation, Star Wars: Clone Wars. Anakin, his protege, originally omits the cloak from his personalized leather Jedi attire, but as he gets darker, he starts donning it as well. He upgrades to the signature black cape and life-support system of Darth Vader after losing to Obi-Wan.
Lucas has explained this phenomenon in interviews. In Star Wars, warm colors and Earth tones symbolize "humanity" (in the inclusive sense) while pure black and pure white both symbolize impersonality. Hence the Empire is entirely black-and-white to signify that it is coldly institutional. Luke wears black to signify that he has become more reserved and withdrawn from daily tumult with his Force training. (However, in the prequels, the Jedi wear earth tones but are some of the most impersonal characters in the series.)
The explanation was made years before the prequels came out. In fact, it has been revealed that originally the Jedi were all supposed to wear black in the prequels, but this plan was ditched because they didn't want the viewers to be confused who's who, and wanted to make Obi-Wan and the rest of the Jedis immediately recognisable as such. Since the original trilogy had established brown cloaks for the Jedi by accident, they had to stick by that to retain the iconic style they had unconsciously created.
Mostly inverted in The Matrix where the good guys were identified by their distinctive black leather trenchcoats. On the bad guys' side, The Twins in particular not only wore white trenchcoats but were themselves albino.
And it fits within the setting considering the main characters are computer hackers and other varieties of Internet geeks, who of course are going to give their avatars cool outfits with long flowing black cloaks.
Hot Fuzz where the Neighbourhood Watch wear black hooded cloaks when committing their murders, but also when holding their meetings which, along with Ominous Latin Chanting, is done for no other purpose than to spoof this trope.
In the film version of Angels In America, Prior wears a sort of modernized cloak (almost a hoodie, but not quite) in each scene after he takes the book (except the one post-Time Skip.) It's quite an attention-grabber when compared to the normal people he walks past. (The play creates a similar effect with a black coat and a scarf that's draped like a hood.)
The killers from Scream films wear black cloaks along with the signature Scream-masks.
The Ghost of Christmas Yet To Come from A Christmas Carol by Charles Dickens, published in 1843, is a rare example of a good (though still scary) guy being a Black Cloak.
Harry Potter: Voldemort's Death Eaters and the Dementors. The Dementor's cloak is all we ever actually see of them; when Harry asks Lupin what's under the hood, he's told that no-one knows for sure, because the only time they lower their hoods is when they suck out someone's soul through their mouth. When they try to Kiss Harry, he sees an Eyeless Face with a toothless, sucking mouth.
In the films, the Dementors are almost intangible (to avoid looking too much like NazgŻl), while the Death Eaters are basically the wizard KKK with their robes the opposite colour.
The books too. Dementors are whispy, drifting, barely substantial shadows that are invisible to Muggles. They are basically Anthropomorphic Personifications of despair, whereas Death Eaters are humans with very warped moralities.
While they're definitely Anthropomorphic Personifications of despair invisible to those who don't have magic, Harry says they look exactly like black cloaks floating; they're probably supposed to look more like the Grim Reaper than "wispy, drifting, barely substantial shadows".
In The Baroque Cycle famous people traveling incognito wear black sashes, anyone who recognizes them is supposed to ignore them while they are wearing the sashes.
Subverted in Don Quixote, when the titular ingenius hidalgo mistakes a group of Benedictine friars for evil wizards.
Somewhat subverted in the Dragonlance novels, by Takhisis, the "Queen of Darkness". Although she has a great many forms (including a giant, five headed dragon) not one of them contains a Black Cloak... Although, the followers of Nuitari, including Raistlin, wear black robes with hoods...
Dracula doesn't wear a black cloak in the book. The cloak originated in the 1924 Hamilton-Deane play and was made famous by (of course) Bela Lugosi.
In The King Killer Chronicles, Kvothe is the main character, and is given one by a member of the fae. Then again, he's not exactly a hero...
Poked fun at in the Discworld book Going Postal, where an experienced con man is annoyed that his underling thinks hurrying through city streets in a voluminous black cloak avoids attention.
The Igor: Allow me to take your highly notithable hooded black cloak thur.
The Auditors physically manifest as gray hooded robes... with nothing inside them.
Also parodied (of course) in Guards! Guards!! by the Mysterious Ancient Brotherhood of ... something, complete with passwords, magic rituals, and much debate between members of the circle.
Averted in The Wheel of Time in a town next to Mordor, where clothing that conceals your face in any way is against the law, because the servants of The Dark One could use them to pass as human.
Not before there were loads of Myrddraal whose cloaks don't even stir however strong is the wind.
The Riftwar Cycle comes at this trope from both sides. To the Kingdom of Isles, the black-robed Tsurani magicians were the most horrible monsters, maintaining the portals that made the war possible and occasionally bringing their unheard-of power directly to the battlefield with terrifying results. On the other side, the magicians were hardly evil and considered themselves loyal citizens, selflessly serving their empire (which itself isn't The Empire after all). And the black robes weren't meant to be ominous - it's just their uniform.
Cowl and Kumori in The Dresden Files. Harry loves making fun of them for their fashion sense. For instance:
Touche, oh dark master of evil bathrobes.
I told these guys yesterday I didn't want to buy a ring.
Bring it, Darth Bathrobe!
Despite that, it does mask their identities, which is probably the point. They can magically deflect attention if they have to, and aren't constrained by the Laws of Magic.
Several characters and organizations in The Death Gate Cycle wear them - the Kir Monks, Sinistrad, the necromancers of Abarrach, and sometimes Lord Xar. Not all these characters are evil, but all have some connection to death or darkness (such as the Kir, a True Neutral religion of creepy but largely harmless death-worshippers).
Inverted in A Song of Ice and Fire with the Night's Watch. Instead of being evil, they guard Westeros from threats.
Mistborn 's Steel Inquisitors wear them as their official uniform within the Corrupt Church's hierarchy. Unusually, they normally keep their hoods down, so their victims can see their faces- particularly, the giant Spikes of Villainy pounded through their eyes.
Richard of the Sword of Truth series acquires one of these. Slightly subverted as it's magic camouflage.
As Gilbert of The Witch Watch notes, 'Why don't cults ever wear yellow robes? It would catch people off guard'
In The Book of the New Sun, torturers - including the protagonist Severian - wear hooded cloaks of Fuligin, "the color that is darker than black". This makes Severian almost invisible in the dark, but attracts unwelcome attention in his home city, so that he has to cover up the cloak. The resultant visit to a costume shop kicks of several major plot threads.
The Duuk-tsarith from The Darksword Trilogy, also known as Warlocks, are the enforcers of the local Corrupt Church, wear all-black robes that obscure their faces, and say very little. Most are unnerved by their very presence.
Many villains in the Shannara series. The Warlock Lord and his Skull Bearer lieutenants from The Sword of Shannara, their successors the Mord Wraiths from The Wishsong of Shannara, and the powerful demon called the Reaper from The Elfstones of Shannara are the most traditional examples. In The Heritage of Shannara, the Seekers (an organization that is actually a front for the Shadowen) usually wear these as part of their uniform, but their leader Rimmer Dall actually usually keeps his hood down and face visible, in contrary to most examples. In The Voyage of the Jerle Shannara, the Ilse Witch and her mentor the Morgawr wear hooded grey cloaks that convey the same general look.
An episode of Highlander: The Series had Duncan being attacked in his dreams by a Black Cloak. He went to a mystic who specialized in this, who gave a lot of psychobabble about the darkness within, and told Duncan not to fight it and try to understand it. It turned out that the mystic was the Black Cloak, and it was a scheme to get Duncan to drop his guard.
Although the Man Eating Plants are hardly trying to conceal their identity, the 2009 remake of The Day of the Triffids clearly draws on the creepiness of this trope by giving the Triffids purple cowl-like hoods which they unfurl cobra-like before striking.
The cult members in Linkin Park's music video "One Step Closer" dress like this. Partially subverted, since curious onlookers do notice a Black Cloaked individual's strange garb and decide to follow him to his hiding place. Hilarity Ensues.
The Archangel Dominic from In Nomine is well known for wearing a black cloak that conceals all and even blocks perceptive supernatural powers directed at him. Whether he's a Knight Templar, a genuine good guy with a really hard job (he's the Archangel of Judgment, responsible for keeping the angelic host free of corruption) or secretly outright evil is up to the individual GM.
The page picture is of the uniform of Organization XIII, from the Kingdom Hearts games, though they tend to pull down their hoods and show their faces unless they're being intentionally mysterious. Said coats have darkness resistant properties, and while Organization XIII mostly just wears them for the effect, characters such as Riku and Mickey wear them to protect their hearts from being worn away by the darkness.
Oddly and ironically enough, Roxas is explicitly told that Organization members should keep a low profile, and make attempts to not be noticed. Even more odd is that the kids of Twilight Town don't seem to find anything suspicious or off about a teenage boy their age wearing a black cloak, or that two people in black cloaks (one, an adult, and the other, the aforementioned boy) are interrogating them.
Of course, from every game after II, every character that's meant to have a mysterious, unknown identity has worn these cloaks, so as to keep a vibe of confusion around the entire series, whether it makes sense for them or not, such as Data Riku.
Also, on the low profile part, it's at least implied that like the Heartless themselves, the wearers are Invisible to Normals.
Though that doesn't stand up well when people like Pence, Hayner and Olette can plainly see Axel and Roxas, along with all the Disney characters the members of Organization XIII interact with.
The Ethereals of X-COM: UFO Defense take them in orange. The image under their autopsy research entry is the only time we see their faces. Subversion: Without the cloaks, they don't look very badass.
In the DS adaptation of Final Fantasy IV, when monsters are represented over the game world (normally during a cutscene) it is through a black cloaked figure.
Happened in the original and the sequel too. Though in those the cloaks are more Blueish.
The Cult of the Damned, as well as Putress, from World of Warcraft. In fact, most cultists in the game, including the Twilight's Hammer and mortals serving the Burning Legion. Best to say that anyone rocking the Black Cloak look in the game is not the sort of person you invite over for tea, even if they're technically on your side.
Putress' attire is actually the warlock tier 8 armour set. Warlock armour often goes for this look.
Darth Revan sports one of these, as well as a face-concealing mask, hakama-pants, and complex armor. Darth Nihilus's costume is all in black and also includes a hooded cloak; Traya as well. Most other Sith in those games aren't quite so concealed - Dark Jedi mooks have hoods and cloth covering their noses and mouths, but no capes.
Of course, the real reason for Darth Revan's mask was that he/she's your player character and you're not supposed to find out about that just because of a few visions.
Purge in Space Channel 5 Part 2 wears a Black Cloak, although he ditches it later.
Rodrigo Borgia in Assassins Creed II, for most of the story, sports a cloak with a hood covering his head. His face is not entirely concealed, but it gives his eyes a sinister glow at times that make him look like a male version of Kasumi Goto. He stops using it after he becomes Pope Alexander VI.
Your character, Ezio, if you dye his clothes black in one of the shops. Altair's Armor is also a black coat of sorts.
In Nightmare Realm, an eerie, fiery-eyed, taloned entity in tattered black robes abducts a little girl from her home.
In Artix Entertainment games there is always the Mysterious Stranger, a being who leads the shadowsycthe organization(s) and desires to bring DOOOOOOOOM upon the world.
Although it's white, not black, Albedo's cloak (complete with wings used for gliding!) from Xenosaga has pretty much the same effect as a black cloak.
Parodied multiple times in Adventurers!. In one case, a character has both this and is sitting in complete obscuring darkness; when asked why, she states that she really needs to get around to replacing some lightbulbs.
A long, black, face-conceling cloak is worn by one of the protagonists of Negative One, Adele, to hide the fact that she is not human.
Used and justified in Girl Genius. The protagonists use this disguise against guards on the lookout for Agatha. The guards recognize it as suspicious immediately, and arrest them. Too bad the heroes expected it, and had dressed up Zeetha in the clock instead, just to check if Agatha could sneak in with such a disguise.
Minister Malack, a lizardfolk cleric of Nergal in The Order of the Stick wears one. Given the presence of Star Wars references in the arc in which he features, his outfit might be a Shout Out to the typical Sith-wear.
And/or another traditional dark-cloak wearing creature...
In The Chronicles of Taras: Red Dementia, Ghost, a five-foot-three-inch high Albino girl, wears this kind of clothing to protect her from the sub-freezing temperature of the black desert and the bright sunlight.
In The Gamers Alliance, both the Totenkopfs and the clerics of the dark god MardŁk wear black cloaks, and neither faction is nice.
In The Graystone Saga, Lady Gray wears one whenever she's out in public, and prefers to keep her hood up. Considering the sort of reaction she inspires in people when they realize who she is, it's hard to blame her.
Prodied in Psychronicles with the introduction of the main characters. It was mainly Rina's idea due to them belonging to a shady agency of supernatural specialists.
In the newer version he spends half of the first episode just in a black cloak with his face hidden in the shadows, presumably for dramatic effect, even thought everyone watching knows exactly who he is and approximately what he's going to look like.
But to counterbalance these, she also wears white after she takes down Trigon and restores all the petrified people to life.
She also wears white when she unites the disparate parts of herself to take down Trigon within her own mind. White symbolizes her having attained "full power" or something like that. There's probably a psychological aspect to it, Raven being psychic/magical and all.
Also white is the color of light before refracted by the atmosphere and divided into color.
Scavenger's first appearance in Transformers Armada has him wearing a cloak that hides most of his body. Why does a robot have a cloak?
Who Killed Who?: The killer wears a black cloak and a black mask covering his head.
Dr. Destiny's mental avatar in Justice League wears a black cloak. In his cameo in JLU, he's physically wearing one.
Truth in Television for the full habit of most Catholic priests, especially those in the religious orders of the Benedictines, the Redemptorists, and the Congregation of Holy Cross (to name a few). The Dominicans are called "the Black Friars" for this reason.
French footballer Nicolas Anelka thought it was a good idea to wear a black cloak after he was expelled for shaming reasons. Well, maybe it kept him from being recognized by other passengers, but he looked really silly when hordes of journalists filmed and interviewed him. Real life subversion? 
Ivan the Terrible's secret police, the Oprichniki, were easily recognizable for wearing black, hooded, monk's robes.