Futari wa Pretty Cure takes this to extremes — the girls' joint Transformation Sequence is a sound and light show on a par with an industrial accident in a fireworks factory, and no one but their current opponent ever notices it — or their equally pyrotechnic attacks.
The attacks are usually unseen because people faint or disappear when the bad guys arrive. The transformation itself is actually instant.
Mahou Sensei Negima! explains that there are spells to prevent normal people from noticing magic and related phenomena. This becomes a major plot point in an early-mid arc where someone wants to invert the spells, forcing people to believe in magic.
In the anime (and part of the manga) GANTZ, during the "games" the main characters and their quarry are literally Invisible To Normals, though they still cause lots of inexplicable blood stains and property damage.
Mai-HiME mildly subverts this trope. While Yukino's power (usually) hides the various supernatural battles from the eyes of the normals, the collateral damage from those battles — often quite significant in scope — remains afterwards, to the concern and puzzlement of many.
And in a further subversion, the damage gets bad enough that the normal students draw the conclusion that the Fuka-academy is too dangerous. Mai's non-hime friends are shown leaving and urge Mai to come along. The campus shuts down late in the series, soon after Mai's Unstoppable Rage over Takumi's death overloads Yukino's attempts to conceal the battle, but it reopens after the final battle, in time for the senior class to graduate.
The Hime Star is invisible to virtually all non-Hime. Natsuki's mother tells her to never tell anyone that she can see it.
Bleach: Spiritual beings such as ghosts, shinigami and hollows are invisible to normal humans but can interact with the world in ways that will be visible. Humans with spiritual power can see these beings but only a few have the power to fight spiritual threats, something at least one hollow has exploited.note The Grand Fisher uses a lure on his head disguised as a vulnerable female child. If anyone sees that child it gives them away as people who have spiritual power, making them good eatin' If humans lose their spiritual power they can no longer see the spiritual world. The sole exception is Uryuu, who mysteriously retained his ability to see the spiritual world despite losing his power.
Shinigami in Death Note can only be seen and heard by people who have touched a Death Note belonging to them.
In CLAMP's X, the super-powered fighters have the ability to create "kekkai" which are barriers that prevent normals from entering, and repair all damage within them when dispelled. However, if the fighter is killed in the battle, the kekkai disappears and all damage immediately appears in the real world.
In Cardcaptor Sakura, there are some beings/objects/dimensions that can only be seen/experienced by people who have magic powers. However, Sakura's older brother, Touya, has the distinction of being the only one who can see ghosts.
In Keroro Gunsou, the aliens and their machines really are invisible, most of the time, thanks to their "Anti-Barrier". That, or they're in a laughably bad disguise that usually reveals their frog-like heads, much like Pinky And The Brain's Man Suit.
In Xxx HO Li C, many of the weird spirits and occurrences that happen can only be seen by Watanuki, Yuko, and other spirits or supernatural beings. Doumeki also eventually gains this ability after he gives half of his eye to Watanuki.
Kohane who is introduced later in the series, like Watanuki, was born with this power.
Mages in Magical Girl Lyrical Nanoha often put up a barrier that puts everything around them sightly out of phase/time to everyone else so they don't perceive the fights held between mages or the latest Monster of the Week. These barriers can, however, be breached and destroyed from the inside.
This trope forms the main premise of Natsume Yuujinchou: Natsume, the titular character, is forced to deal with several supernatural creatures that only he able to see which causes him a lot of grief, eventually turning him into a verylonelyperson.
In A Certain Magical Index, magicians regularly lay down barrier spells/runes to prevent normal people from seeing them and what they do. One likens it to the world being a coin, where normal people are standing on one side and magicians are on the other. Most of the time, this effect is achieved with a spell that makes normal people simply leave the area.
Ghosts in Rinne are invisible and intangible, and the hero has a coat that can do the same to him. It has the opposite effect when you turn it inside out.
The Season Fairies in A Little Snow Fairy Sugar can only be seen at special times by special humans. In fact, after the fairies find all their Twinkles, their human companions lose the ability to see them. This, of course, happens to Saga.
In Sugar Sugar Rune, only witches and wizards can see magic spells being cast. Everyone else is "frozen" until the incantation is complete.
In JoJo's Bizarre Adventure from the third arc onward, the metaphysical 'body' of a Stand is only visible to other Stand-users. This makes Hayato from the fourth arc a particularly impressive character in that he provides invaluable assistance to the heroes despite only being able to perceive Stands through their effects on the physical world.
Rozen Maiden. In season one, Jun goes researching Rozen Maidens on the internet, only to find that nobody believes they exist. Yet, Sugintou goes flying in broad daylight in a busy city and nobody notices her. The dolls travel from place to place in flying doll cases- again in broad daylight. Logically speaking, SOMEBODY would have to notice the aforementioned occurrences. Yet, the only people who actually know about the dolls are the mediums/others they live with.
In Yu-Gi-Oh! GX, Duel Monster Spirits are invisible to most people. What determines who can see them isn't really ever explained, and only a few individuals are even confirmed to be able to see them. Juudai, Hayato, Johan, Manjoume, Fujiwara, Edo, Satou, and Geise could all see spirits, though Hayato, Satou, and Geise were implied to only see their own personal ones, and Edo said he could see strange things after his third duel against Juudai.
In YuYu Hakusho, most demon bugs and some demons can only be seen by people with high enough spiritual sense. Koenma uses this as an advantage to give out information to his detective and friends without the fear that muggles might see.
The mushi of Mushishi can only be seen by certain people.
A few smaller examples are abound in Axis Powers Hetalia. There's all of England's "magical friends" (Unicorn, Flying Mint Bunny, Brownie, and an assortment of fairies and other magical creatures) of which only he can see (and a few select others such as Norway and on occasion France, though only when in England). Then Japan's Kappa, which only England can see as of the present, and presumably Norway's Troll. Though it's been said that everyone (but America, except for on Halloween) can occasionally inherit England's second sight when visiting the nation, England and Norway are the only ones with the ability to see the magical creatures which are invisible to normal people.
Much of what the runaway spirits in The World God Only Knows do can't be seen by people who aren't either supernatural themselves or linked to it by being a buddy or host. Other things aren't this convenient and do have to be hidden somehow. Causes a real problem at the end of the Hinoki arc when Fiore more or less toggles the invisible off in regards to Hinoki's giant form and causes an event so large that Hell can't entirely cover it up and instead have to turn it into an urban legend that simply has no physical proof.
In Kiniro No Corda, the protagonist Kahoko can see Lili, the fairy of her high school, which is something only a few can do. Lili was so happily surprised she gave Kahoko a superpower...sort of.
Among the powers of Helen of Helen ESP is the ability to see various otherwise hidden supernatural beings.
In Berserk, normal people, especially those who are dedicated to the Holy See's religion and those who have never had a supernatural encounter, can't see elves. As Puck attempts to explain, when a person looks at something, they imprint the event in their memory and they remember it, but if they don't remember what they've just seen, then they only try to remember the good parts of that event. A simpler explanation would be that when the secular religion took over the pagan beliefs, it all became a matter of clapping one's hand to believe, and the populace only see stuff that they want to see.
The main character in Noragami can only be seen by the main heroine, who saves him from getting hit by a bus. When she recovers, the people who were at the accident remark that there was nobody there besides her.
In Kill la Kill, Ryuko's superpowered uniform Senketsu is sentient, but normally, only she can hear his voice, leading the others to think he is her Imaginary Friend or Companion Cube. At one point, Senketsu directly gives Tsumugu a threat and he's surprised to actually hear him. Ragyo and Satsuki can hear him as well.
In Fables, there's an outright war on the streets of New York between the forces of the Adversary and Fabletown. They explain that there are many magical protections to keep "mundies" out of Fabletown (or just walk through, in cases of days where there isn't a gigantic battle) but the spells had to be weakened in order to cast another spell: a rainstorm to put out the fires. It's then noted that the rain will keep people out of their business and reduce visibility enough that, if they can finish the battle fast enough, nobody will notice anyway.
In Monster Allergy, monsters can be only seen by people who have the Sight Dom. Tamers and Keepers are those people who can see monsters.
In Ultimate Fantastic Four, the Argiopes are spider-like creatures who attack the sources of time paradoxes to protect the timestream, and can only be seen by time travelers.
Zatanna once asked for Superman's assistance against a portal that was spewing out demons. While Supes could see and fight the demons, he couldn't see the portal, even after going through all his different vision modes. Zatanna goes, "It's outside the electromagnetic spectrum!" and uses a spell to make it visible.
In The Best Seven Years, Hobbes is a Furry. Furries are magical versions of regular animals born from said regular animals. They possess the traits of the animal they are, along with human traits such as speech and walking on two legs. Furries, however, can only be seen by wizards: Muggles see Furries are regular animals, or in some cases (Like Hobbes) as an inanimate version of that animal.
Nick in The Invisible can only (barely, sometimes) be heard and felt by the girl who has almost killed him. And by animals. To everyone else he is invisible.
In Oh, God!, God cannot be seen, heard, or recorded by humans unless He allows it. This even extends to transcripts, such as a stenotype paper record of His courtroom testimony.
In Beetlejuice, ghosts typically cannot be seen. However, the Goth girl Lydia can because she is, in her own words, "strange and unusual".
In The Sorcerer's Apprentice, magic itself is invisible to normals, as demonstrated by Becky's inability to see a giant flaming pentagram above the city. Magic that creates physical effects, such as starting a fire or animating a statue, is visible, since the objects themselves are otherwise normal.
In Icelandic folklore the Hidden People are a race of people that are invisible to humans, unless they wish to be seen. Oddly enough, they would also be invisible to one another if it were not for a salve that is smeared in the eyes of their newborns. Normal humans only know this because the Hidden People tend to lack midwives, and thus seek humans' help when in labour. The human midwife would then be asked to smear the salve in the infant's eyes, and would then accidentally get some of the salve in one of her own eyes. From then on she would then be able to see the Hidden People and their world with one eye. Often resulted in madness...
Played with a bit in regards to most magical locations. To keep Muggles from discovering magic, most wizarding locale use some sort of enchantment to keep Muggles from wandering into them, which includes spells to make them look like something else entirely (for instance Hogwarts, which will look like withered ruins to any Muggles that find it), repel them from the areas in question (the Quidditch World Cup's stadium), or to keep them from noticing the spot at all (The Leaky Cauldron). There are also things that even most wizards can't see, such as thestrals (horse-like reptilian beings that are invisible unless you've seen someone die) and any location protected by the Fidelius Charm (which keeps you from seeing a particular location unless you've been told the address by the Secret Keeper).
Fablehaven has certain creatures that only those that are "fairystuck/fairykind" or "shadow charmers" can see,one jarring instance was a kobold who disguised himself as a cute guy and dated all the girls in Kendra's class despite being a goblin with us leaking out the side of his head
In the novel and miniseries Neverwhere, people who live in the London Underground are effectively invisible to normal people. These people can stand in front of normal people, completely naked and actually trying to initiate some sort of conversation, and be utterly ignored. On the off chance they are able to grab someone's attention, they are almost always promptly forgotten. Played for laughs in one scene where museum security is called on to remove Richard, only to spend about half an hour trying to figure out just who they're supposed to arrest.
In Terry Prachett's Discworld novels, Death actually explains this. It isn't that the normals can't see them, it's that the normals' brains come to the logical conclusion that they CANNOT EXIST and therefore write them off as not existing. It's important to note that this only happens to adults. Children, who aren't educated and mature like adults, are imaginative enough to see what's really there. Wizards and Witches can also see them: both because they're magically attuned and because they're entitled to a personal visit when their time comes.
Death's "granddaughter", Susan, inherits some of this talent in that she can make other people ignore her. When using it generally, she won't be noticed by normal people unless they focus their attention, but those of magical persuation (like wizards) can still sense that someone's altering perception and use that to focus on her. However, once she knows someone's onto her, she can concentrate on that person, and even Archchancellor Ridcully can't pick her up once she knows he's trying to seek her.
In Cassandra Clare's Mortal Instruments, Shadowhunters, demons, and Downworlders are all invisible to normal people, or 'mundanes', until they've been bitten by a werewolf, forced to focus, or otherwise pulled in.
In the Percy Jackson and the Olympians novels, most mortals can't see most mythological things because of the Mist, which is apparently some sort of Weirdness Censor. The Mist lets them see something more "normal" than the mythological reality; for example, a three foot long celestial bronze sword might be perceived as a shotgun, or the massive hellhound that just busted through a solid brick wall could look like a poodle. There are some mortals that can see through the Mist, but they are few and far between. The Mist can also be manipulated to make people think or see certain things. And Mount Olympus is accessed by a special elevator to the 600th floor of the Empire State Building - which makes some New Yorkers wonder how it can be Hidden in Plain Sight at the cruising altitude of airplanes.
The Bartimaeus Trilogy by Jonathon Stroud takes place in an Unmasqued World, but this trope still applies somewhat: demons can change their forms and often do, though their true selves can be seen on "higher planes." Demons can see on multiple planes to recognize each other; magicians can use special contact lenses to see on a few and are thus harder (but not impossible) to trick.
In Twilight Eyes by Dean Koontz, creatures called Goblins can only be seen in their true forms by humans with some psychic ability (the "Twilight Eyes" of the title). The main character has unusual purple eyes that make him able to see them. Another character has an amber third eye in his forehead with the same ability. The protagonist's love interest can also see their true form and see the future, though there doesn't seem to be any visual quirk to indicate it.
According to the Star Wars Expanded Universe, people who are not Force-sensitive cannot see or hear Force Ghosts. For example, during Star Wars: Legacy, Cade Skywalker is contacted by the Force Ghost of his ancestor, Luke Skywalker, but Cade's companions think he's talking to himself.
It also happens in Galaxy of Fear: Ghost of the Jedi, though initially even Tash can't see Aidan either, just sense that he's there and watching. She gradually becomes able to perceive him more and more clearly. When she's trying to enlist his help while being threatened, the Big Bad says that acting crazy won't save her.
In Junior Jedi Knights: Anakin's Quest, Anakin Solo, Tahiri Veila, and Uldir Lochett enter the Dagobah cave. While Anakin and Tahiri experienced horrifying visions, Uldir only perceived it as a cave, because he wasn't Force Sensitive.
In Septimus Heap, the door to the Queen's Room is visible only to the Queens and Princesses.
David Eddings' The Elenium and The Tamuli actually show three different ways to achieve the trope, each by a different supernatural force. Styric Child-Goddess Aphrael can cast a spell that makes people ignore her and anyone else with her. The Delphae Xanetia can alter the light around her, causing it to "wrap" around and pass her. And the the Troll-Gods somehow come up with a weird third way. In essence, they jump from one frozen moment to the next. To someone within, it looks like the world is going at something like 1 frame per second, with all the jerkiness that implies. Meanwhile, the rest of reality never gets to see the people inside because the instant they're visible is vanishingly small. Interestingly, due to the differing magics involved, method #3 seems to interfere with method #2 (someone in the skipping invisibility will see Xanetia with a multicolor glow).
Inverted in "The Devil's Footprints" from 13 More Tales of Horror. Everyone at the party can see the mysterious goat costume guy, but Brian the house-controlling computer cannot see him on the camera footage.
The 200 million horsemen army in the Left Behind book Assassins is invisible to everybody but believers in Christ, but are nonetheless dangerous to those who aren't believers, as they have been unleashed to slay a third of the remaining world's population around the time of the Sixth Trumpet Judgment (believers not included).
In John Dies at the End by Jason Pargin (a.k.a. David Wong) the majority of the monsters John and David battle are invisible to most humans. This is because the monsters are from another dimension and their existence extends to this one by varying degrees. Those that can see them are either psychic, not human, really drunk and stoned with an open mind, or in John's and Dave's cases have taken the drug "Soy Sauce", which tunes your brain into the different "frequency" these monsters exist in.
Pact explains the lack of noticing Others by normal people as a result of the Standard of Suleiman bin Daoud (the Biblical King Solomon), an agreement that most Others, over the course of the past several thousand years, have been forced to sign by various practitioners that bound or negotiated with them. The Standard means that Others can't interfere with the uninitiated without some excuse-failing the test of a sphinx, or wandering where a goblin might find them instead of staying home.
Live Action TV
Throughout the seasons of Fraggle Rock Gobo spends a lot of time ducking out of sight from the resident human, Doc... only to discover in the penultimate episode that under normal circumstances humans can't see Fraggles anyway, so he needn't have bothered. To add insult to injury, this is also the one episode where Gobo actually needs Doc to see him, so he has to work out how to make himself visible to the human. The "Youcan See Me?" event happens in the last few minutes of the episode.
The Last Great Time War in Doctor Who is an example - in "The Unquiet Dead" it is stated that the War was invisible to lower races, but devastating to higher ones, particularly those who were time sensetive.
The perception filter can also act like this; however, 'normal' means 'not in on the secret'. People won't be able to see that rather out-of-place Police Box unless they know to look for it.
Weaponised in "The Sound of Drums" and "Last of the Time Lords", where the perception filter prevents anyone from noticing The Doctor, Martha and Jack during their attempt to hide from the Master, as well as allow Martha to organise La Résistance while the Doctor enacts his Gambit Pileup during The Year That Never Was.
Happens repeatedly to Annie the ghost in Being Human. Most ghosts can only be seen by other supernatural creatures—for example, the new tenants of Annie's flat, a werewolf and a vampire. However, as time goes on, Annie begins to become more solid and visible, at one point able to pass as a living human again. During the transition, however, there's a lot of "Can you see me?", and George actually uses the phrases 'invisible to normals' at one point.
At one point, Dean of Supernatural gains the ability to see those possessed by demons for what they are. This occurs when he is running out of time with his Deal with the Devil.
Hellhounds and Reapers are also invisible to normal humans, and can only be seen by the people they're coming after.
Happens accidentally to Daniel in the episode 'Crystal Skull' of Stargate SG-1. This leads to a funny conversation between Daniel and his grandfather (who can see him due to having encountered the same phlebotinum skulls that turned Daniel invisible): neither realizes they're actually talking to each other at first, as his grandpa thinks Daniel is just a hallucination but talks back anyway, and Daniel doesn't expect an answer and is just responding to conversations to pass the time/rhetorically, as no one else can see or hear him.
Also occurs in a number of other episodes, including one in which a young boy who arrives on base is revealed to be able to see an invisible race, and was genetically created to have this ability.
There's also an episode where SG-1 activates an alien machine that allows people to see invisible creatures in another dimension (and forget how to use their brakes.) This understandably freaks-out the residents of Colorado Springs.
In the episode which fans do not refer to by name, an malevolent entity impersonates Al for most of the episode, then turns to acknowledge the real Al when he finally manages to show up. Sam and Al are naturally freaked out.
Grimm has Wesen, supernatural creatures, whose true form is visible to Grimms when they are under stress or undergo other strong emotions. To everyone else, they appear human except in rare instances when they actually want to be seen, and even then the person has a hard time processing it.
Changeling The Dreaming has chimerical items and beings, creations and creatures of the Dreaming that can only be perceived by the fae or the people they enchant. In keeping with the game's themes, these things can affect you, but trying to affect them back - or even just taking the blow - can make you look nuts to mortal observers.
In The Addams Family musical, the chorus of ancestral Addams ghosts can only be seen by the family. This leads to some amusing situations; for example, near the end Wednesday catches a bouquet thrown to her by a spectral bride, much to the confusion of her "normal" fiance.
In Silent Hill 2, the little girl Laura is the only one who doesn't see the monsters or how scary the town looks. This is actually a deconstruction of the trope specifically because she's normal, meaning she's the only one who's sane.
The Thief series strongly suggests that Keepers are Invisible to Normals when they want and only gifted people, such as Garrett, are able to notice them.
Talented hiders would know where to look for the hiding places Keepers would use. This may overlap with Invisible to Adults, as Garret was just a street urchin when he attempted pickpocketing a Keeper. This Origin Story is bookended at the end of Thief 3, when Garret, now the leader of the Keepers, catches a young girl pickpocketing him and gives the same line.
In The World Ends with You, the Players of the Reaper's Game are invisible to living people, except when they go in shops to buy things. The Noise are also invisible. However, it is implied that there are some people who can see the Game, such as one bystander whose thoughts reveal that he can see Noise symbols. He calls them "weebers." Weebie weebie weebie... Another one mentions that she saw someone with wings.
Actually, only Colette and Yuan can see Tenebrae naturally. Tenebrae can turn himself visible, which lets the other party members interact with him.
Shadow Pokémon in Pokémon Colosseum have a black, fiery aura that is invisible to everyone except the girl who, conveniently enough, is your traveling partner.
In the sequel, the Aura Reader was designed as a means of detecting this aura for the more mundane protagonist - one of the obstacles for purification is the ability to identify Shadow Pokemon reliably and immediately.
Throughout the franchise, Normal-type Pokémon are immune to Ghost-type moves and vice versa.
The devils in Devil Summoner 2 - Raidou Kuzunoha vs. King Abaddon certainly apply. Raidou can summon a devil to follow him around, and even send it out on solo missions, but most people are blissfully unaware.
In Golden Sun, the protagonists use Psynergy, which is basically magical abilities, which can only be seen by those who can use it. However, at one point you fight in an arena against a series of opponents who are standard humans, leading to some Fridge Logic for what the audience and opponents see when all these gladiators are defeated by a character who just waves his hands around to damage his opponents.
Subverted by Briggs in Dark Dawn, when he identifies Matthew & Friends because he saw them handwaving around some crates on the other side of the dock and realized it must be Psynergy. Possibly the exception that proves the rule, since Briggs knows about Adepts and Psynergy already and would know what to look for.
Heavily subverted in City of Heroes. Normal citizens will be able to see you use magic, supertechnology, etc. They will come up to you and thank you for beating up the mobs that were being jerks. And if you're playing City of Villains, they will cringe away from you.
Although Amaterasu from Ōkami is not Invisible to Normalsper se, to most people she appears as nothing more than an ordinary wolf rather than the flaming bronze plate-equipped, red-striped mother goddess of the sun.
In Ancient Domains of Mystery, a number of foes, including the Cat Lord, are invisible, requiring a means of seeing invisible in order to defeat easily. The player can also become invisible, making most enemies incapable of seeing the character, with a notable exception of shopkeepers, who can sense the presence of an invisible character if given sufficient time.
In The Legend of Zelda: Ocarina of Time, Link needs to uses the Lens of Truth later in the game to be able to see hidden doors, objects, monsters and a boss. One NPC in the game also claims it's possible to see such things by extensively training one's mind, but of course, doing this in the game isn't possible.
Venat in Final Fantasy XII, and perhaps the rest of the Occuria, too. This is, in fact, part of the reason that Dr. Cid comes off as being mad, as he carries out conversations with Venat as normally as with anyone else, though to nearly everyone else, it appears as though he's talking to himself.
In The Elder Scrolls V: Skyrim, despite anyone being capable of reading the Dragon-Language inscriptions on Word Walls, the Nordic denizens of Skyrim have puzzled for millennia over what their true function was. It's implied that only the Dragonborn is capable of percieving the hidden Words of Power written upon them.
In Mass Effect 3, Shepard is able to understand the Prothean data recordings found on Eden Prime, which everyone else only percieves as noisy static, due to having the collective knowledge of their race implanted in their subconscious during the first game.
The main character in Otherworld: Spring of Shadows needed a special amulet in order to see fey creatures (good and bad). In Otherworld 2: Omens of Summer the "sight" was temporarily granted to her by the little girl she'd spent the entire first game trying to find.
In Contrast, only Didi can see Dawn. Also inverted, as Dawn can only see Didi - other people can only be seen by their shadows.
The gods of A Moment Of Peace are invisible to the stick figure humans they walk among, but apparently Monster Food, worm like creatures hanging from the very bottom of the food chain, can see them.
Somewhat Lampshaded in MegaTokyo. Some people in the strip notice the giant drunk turtle, the zombie hordes, and the rent-a-zillas, but most are blissfully ignorant. Ironically enough, the one whom is the most out of touch with reality, Largo, is not only able to see them, but seems rather capable in dealing with them.
Since the TPD has an entire division dedicated to organising, managing, and cleaning up after the giant drunk turtle, zombies, and rent-a-zillas, you could argue that in Megatokyo, this IS normal life, and everyone's just resigned to it.
It's later revealed that average people have a "SEP Field" that prevents them from seeing the extraordinary things in Japan (giant monsters, magical girls, Ninja, etc.). Only those who have had the field shattered (Junko), are a member of the extraordinary (Miho, Yuki, Meimi), or have a very blurred view of reality (Largo, Dom, Ed) are able to see things for what they are.
The whole thing is unclear. For example, at the same time as Junko is finally noticing all the weird things that are happening around her, a guy is complaining that if she had been paying attention, a robot wouldn't have smashed his car with a telephone pole. It seems more like half the people notice but don't care, and the other people don't notice.
Actually its more like each person has a unique perception filter. While Largo can see zombies and the like, he also sees zombies where there are none. Like raves.
In The Dragon Doctors Tomo Wakeman is a ghost who is not only invisible, but completely unnoticeable unless she, say... intentionally stomps on a shaman's toes.
Gradually subverted in Fans!, where despite the best efforts of the sinister shadowy Government Conspiracy the truth of what really happens eventually becomes public knowledge.
In Gunnerkrigg Court, the psychopomps are able to reveal themselves to anyone, but usually operate invisibly, since they're forbidden from interfering in the lives of mortals. However, some etherically-gifted individuals—including Antimony and Surma—can see them even when they're supposed to be invisible.
The RoTD plays this... weirdly; while Mort and Annie see the requisite occult and arcane trappings, Kat only sees the whole set up as a sort of kitsch haunted house causing her companions to be amazed at her ability to navigate and operate such eldritch mechanisms as a VCR and camcorder.
The town of Mayview from Paranatural is haunted by numerous ghosts and other supernatural creatures, which only a few people can see.
In theParadise setting, human characters are randomly, permanently changed into Funny Animals (and some are gender-swapped as well). After they Change, characters have an illusory full body disguise of their old human selves where normal human beings are concerned (whether they like it or not), especially early on when the "Reality Distortion Field" is stronger. A man who turned into a female bear might look much like his old masculine self, just a little overweight—which means he will need to continue to dress like a man. Normals literally cannot tell anything has changed; only other Changed can see them as they are.
It seems the Slender Man is only seen when he wants to be seen and rarely shows himself to anyone besides his victims. People who don't know about him are usually safe. Thus, even if he were near right now, perhaps even looming over your shoulder as you read this, you wouldn't be able to see him.
The gods and demigods in Thalia's Musings, unless they choose to be seen and/or heard. Thalia claims to have used this power to stalk mortal men.
In the Addergoole setting, a double layer of invisibility exists: fae can Mask to hide their unnatural appearance from other fae or fae-blooded, and something called the Blindness of the Gods hides such things from normal Mortals. Except on Halloween
Possibly the Ginosaji in The Horribly Slow Murderer with the Extremely Inefficient Weapon series. No one but his victim Jack seems to notice the creepy guy with white makeup and a black hoodie hitting someone with a spoon. When Jack tried to take a photo of the Ginosaji, the only thing that showed up was a strange blur.
In Worm, parahumans gain their powers by connecting to a strange, extradimensional entity which does the heavy lifting for them-giving them Required Secondary Powers and influencing them to be more effective in combat. Chevalier of the Protectorate can see images of these creatures when he looks at parahumans thanks to his power.
Demona in Gargoyles occasionally used magic spells to prevent mundane people from noticing her or her accomplices. This eventually was done away with when she gained human shape-shifting abilities. Goliath and the other gargoyles simply relied on Plausible Deniability to keep themselves hidden, but eventually they were seen enough that the Masquerade fell.
Any member of the third race can do this as well, though usually they just shapeshift into a human form.
The Transformers made themselves Invisible To Normals by hiding in plain sight. Nobody's gonna see a VW Bug on the road and jump to the comclusion that it's an alien robot, after all.
Multiple media have had the fact that Transformers do not have a driver eventually draw the attention of humans. Most notably in Car Robots/Robots in Disguise, where the desperately unlucky Kelly often winds up in the crossfire between the Autobots and Predacons. She does not see them transformed, but starts being seriously freaked out about these strange cars driving themselves. (It doesn't help that her own car was an Autobot, who dumped her and drove off in the first episode.
Of course, the newest comic series has fixed this problem by giving them the ability to project hard-light driver holograms who not only help them hide out but provide a vehicle (haha) for their interaction with humans while in their camouflaged state.
The first Transformers comic book series had the Autobots deploy inflatable human dummies for the same purpose. The dummies could hand give credit cards to gas station attendants to pay for gasoline...
In the 1980s cartoons, at least once the humans who knew about the Autobots helped out by 'driving' one.
In the final battle of W.I.T.C.H., the heroines are forced to fight in downtown Heatherfield. Normally, such a battle would be easily noticeable, but the girls get around this by having three of their friends create, as Will put it, "one ginormous glamour zone" around the battle, making it appear to anyone standing nearby that the fight is merely a cartoon taking place on a large television screen which has been recently built on a nearby building. Of course, in order to maintain this illusion, they must still prevent any debris knocked around in the fight from crushing the people below.
The Life and Times of Juniper Lee has it so only specific people can see supernatural happenings. Only people who are magical themselves can see magical beings, due to a 'veil' erected by the 'elders'. One of Juniper's tasks is to enforce this separation.
In the animated movie Ferngully, humans can't see fairies unless a fairy grants them "fairy sight."
Not necessarily. It was Crysta miscasting the 'sight' spell as a 'size' spell that got Zach in his initial predicament. He seemed to see her glowy self just fine before that.
In The Smurfs, Smurfette's pegasus friend Blue Eyes is only visible to Smurfette, which makes other people including her fellow Smurfs think that her friend is imaginary.
Angels Friends, Angels and devils can't be seen, heard or touched by humans until they take on human form. Though Raf isn't sure if this applies to dogs too...