Naru of Sailor Moon blatantly tells Usagi to be careful before she goes off to fight the Big Bad in R. Usagi tries laughing it off but it's obvious to the viewer that Naru already knows.
In Sailor Moon S, Usagi goes for a drive with Haruka and Michiru, has the exact same conversation with them as she had with Uranus and Neptune a few episodes earlier, and even mentally superimposes Uranus's face over Haruka's, realising that they look exactly the same. She forgets all about this a few minutes later and it's a big shock when she eventually discovers that Haruka and Michiru are Uranus and Neptune.
Mamori in Eyeshield 21, generally one of the smartest characters in the series, is only able to imagine that Sena and Eyeshield don't like each other when she realizes that they're never around at the same time. And when "Eyeshield" accidentally calls her "Mamori-nee", appropriate since the two have been friends since childhood, Mamori of course thinks that Sena must have told him to call her that. Apparently, she's so used to thinking of Sena as an unathletic, unassertive pushover, she only found out after Sena removed his helmet in front of her.
Ranma 1/2: Akane Tendo with regards to P-chan's true identity. Several other characters fall victim to it as well, including one who actually sees the transformation of two individuals he views as separate, but in that case it is heavily mocked by the rest of the cast.
In a notable subversion, Ranma's mother, Nodoka, starts figuring out that her son and "Ranko" are one and the same all on her own, and as soon as the coincidences start to pop up.
Deeply subverted in Magical Project S. In the final episode, the panicked sidekick runs into the heroine's classroom and tells her she needs to transform into her superhero form right away. She's horrified to realize that her identity has been revealed in front of all her classmates...but they just shrug: "We've known it all along. After all, you and the costumed superhero look the same, have the same voice, the same personality, and almost the same name. We just didn't say anything because we figured it was supposed to be a secret."
Ran from Detective Conan almost figured it out in the first volume, with many other close calls. Fifty-eight volumes later and she's still clueless. Justified considering all the calls she's gotten from Shinichi, and the fact that shrinking to the size of a six-year-old is ridiculous, and that one time she thought she saw Shinichi and Conan in the same room...When you get right down to it, Ran's no Kogoro is clever but she's not in Conan's league. Every time she's obviously suspicious, Conan will always be able to figure out some way to outsmart her. (There's also the setting's otherwise realistic Weirdness Censor to consider. It's so obviously ridiculous that someone could youthen, she'll immediately jump at any reasonably plausible alternative.)
Early in the Buu saga in Dragon Ball Z, Gohan, who usually untransforms from Great Saiyaman on the school roof, accidentally does so in front of a girl, who he is then forced to date (and do whatever she wants) so that she'll keep his secret: that he wears teddy bear underwear. She didn't see any of him as Great Saiyaman because she didn't have her lenses on.
Kankuro – Talking while a Photo Montage of him being CurbStompBattled by a smiling Miki: But everytime, my attacks have failed just barely. Everytime, I’ve lost just by a hair’s breadth, nya!
Tsukiumi from Sekirei unknowingly lives with her masked rival for months without cluing in. When she first meets him as Kagari, she comments that he "looks familiar", but fails to put the obvious together. She eventually puts two and two together, after Kagari attempts to kill Minato with a fireball ......but only after she realizes there's only one Sekirei with fire-powers, and Musubi states that she once saw a masked man that looked like Kagari from behind.
Comic book subversion: In Ultimate Spider-Man, Kenny figures out who the titular hero is early in the comic's run, and though he tries to shake the trail by actively ignoring his Spider-Sense, it's shown much later that Kenny's still sure. In fact, when he calls Peter on it, he assumed that everybody knew and it was an Elephant in the Room.
In the Darkwing Duck comics, Drake Mallard and Megavolt are working at the same company. Megavolt notices some similarities and grills Drake Mallard about it, but immediately drops it when Drake says that he's never had the desire to "dress in purple and enforce his own twisted sense of justice."
Lex Luthor has at least once rejected clear evidence that Clark Kent is Superman. Why? Because he cannot comprehend the idea that a being so powerful would adopt such a pathetic alter ego.
Done straight in Superman Returns, apparently as a Lampshade Hanging of Clark Kenting; Lois Lane and her fiance are discussing Superman, as Lois rattles off some of the hero's traits, including his height. Her fiance then looks at Clark, and asks Lois how tall she thinks he is. As they're looking thoughtfully at him, Clark "notices" them looking, gives a profoundly dorky wave, and they say "Nah..." and laugh.
In the comics, Lex Luthor hired a detective to find out all about Superman; she quickly came to the conclusion that he was secretly Clark Kent, only to have Lex fire and discredit her for making the laughable (to Lex) suggestion that someone with so much power and public adulation would lower himself to pretending to be a common man on the street.
At one point in the MAD parody of Superman II, Lois Lane realizes that Clark Kent is never around when Superman is, and confronts him with the obvious truth: "You're deliberately avoiding him!!"
Lois comes this close in the original Superman movie, too, noticing that Clark never seems to be around when Superman is... no, never mind, that's just too crazy.
There's a version of this trope in Spider-Man. During the Norman Osborne funeral scene, where MJ and Peter kissed after she confessed her love for him, he told her they could only be friends. When he walks away, she has this BSOD look on her face as she touches her lips. It seems she suspects who he really is.
Subverted in Ultraman, where the main protagonist knows he can't keep the charade up for long as the team gradually becomes more and more aware of his mysterious disappearances. In one case, once the monster of the week has been defeated, they cynically state "Isn't this the part where he shows up again all of a sudden?"
Also happened to Bulk and Skull in Mighty Morphin' Power Rangers whenever they came up with a Zany Scheme to discover the Rangers' identities. At no point do they ever consider the fact that there are a group of five (occasionally six) teenagers standing nearby that only ever wear the Ranger's colors, have the same voices, and have martial arts skills.
One episode of Forever Knight has Schanke come very close to deducing that Nick is a vampire. His investigation takes him to The Raven, where Jeanette tries to hypnotize him into dropping the idea. She fails, but when Schanke gets to CERK and talks to LaCroix, the old vampire convinces him that he's being irrational, trying to rationalize Nick's eccentricities and downplaying their partnership. Schanke gives up on convincing himself that Nick's a vampire, settling for the fact that Nick's a good cop and a good friend.
And then they Dropped a Bridge on Him to ensure that the question never came up again. He gets replaced with a girl who quickly learns that vampires are real, but never figures out that her partner is one.
In the first episode of the second season of Hannah Montana, child prodigy Rico starts high school the same day as Miley & Co. and blackmails Miley into being his girlfriend by threatening to reveal her secret. Too bad it's the wrong secret...
In a later episode, Rico gets closer when Miley uses some of Hannah's dance moves in school. He is reminded of Hannah Montana, but plays this trope straight by deciding that Miley "isn't smart enough to pull off a double life."
Arthur in Merlin. He is aware that Merlin is smarter than he looks, believes that he's got something to hide, and often seems to see through Merlin's Obfuscating Stupidity. This extends to other characters, such as The Beginning of the End when he seemed unsettled after learning that the Druid boy he saved was Mordred despite the fact that he hasn't done anything villainous yet (both in-show and to Arthur's knowledge). And yet he always thinks It's Probably Nothing.
Roxane: Refuses to believe every single evidence that Christian is not eloquent or that Cyrano loves her. Here is a list In Act III, Roxane comments to Cyrano that sometimes, eloquence abandons Christian. Then accuses Cyrano of being jealous of Christian… because Christian is a better poet than Cyrano. Christian loses his eloquence again and Roxane rejects him; somehow, Christian gets his eloquence again, only then Roxane notices he speaks with another voice. She doesn’t find anything odd about it. In Act IV, Roxane finds it strange that Christian seems shocked by the notice that she loves him for his soul instead for his beauty. Roxana then deduces… that Christian is a Master of Delusion himself! Also, she does not find it strange that Cyrano asked her three times if she could love an ugly man. Nor that in Act V the guy who visits her without fail every Saturday for 14 years could have different feelings for her than Just Friends. Averted at last when she hears the same voice from 14 years ago when Cyrano reads Christian’s last love letter, at night. Justified because Roxane is a Daydream Believer who seriously wants to live a romance with a fair, witty hero, like the D’Urfe novels she has read.
Cyrano: In Act I Cyrano states that he does not believe that even an ugly woman could love him, much less beautiful Roxane. In Act IV, when Christian confronts him with Roxane's confession that she loves Christian soul instead of his beauty, Cyrano doesn’t believe and answers that if he confessed, Roxane would not love him. Then Cyrano averts this trope when his cousin assures him she would love Christian even if he were ugly…three times. Justified because Cyranohasseriousissues.
Averted by Christian: In Act II, Christian notices that Cyrano is too eager to be Playing Cyrano… Cyrano deceives him. In Act III, Christian feels that something about the plan is wrong… Cyrano forces him to follow the plan. In Act IV, Christian finds it strange that Cyrano weeps on the love letter for Roxane and that Cyrano risks his life walking through enemy lines to send letters to Roxane twice a day. Christian discovers the obvious truthand forces Cyrano to tell it to Roxane.
Valerie of Danny Phantom started to notice odd things about Danny shortly after becoming The Hunter ("Where's he running to all the time? Only guys I see running off like that have a job..."), but it never led anywhere (in the real timeline, anyway).
The following exchange occurs between Daisy and Frieda on Static Shock after Virgil and Richie run off after hearing a siren:
Frieda: Look! It's Static and Gear!
Daisy: And, as usual, Virgil and Richie are missing out.
Ram-Man: Uh... how come we never see Prince Adam when He-Man is around?
In He-Man and the Masters of the Universe (2002), one episode ends with Teela questioning why a dragon spared He-Man's life after beating him in a fight. When it is suggested that it did so because its life had been saved earlier that day, she points out that it was Adam who saved it, not He-Man. Man-At-Arms is only able to maintain the Masquerade by hastily turning the situation into an Aesop.
Played with in one episode of Batman: The Animated Series. Newly released from Arkham, Harley Quinn is out shopping when she runs into Bruce Wayne. She stops him, then covers the top half of his face, saying, "I recognize that chin..." and then declares, "I knew it! You're Bruce Wayne, boy billionaire!"
Taken to extremes for laughs in WordGirl. Becky almost gets caught in several episodes—including one where her cape is actually sticking out from under her clothing (she's only able to throw off her friend by purposefully flubbing a "vocab bee") and another where a villain tricks her into flying in front of her family—then accidentally zaps away everyone's memory, including his own. Even her parents begin to put the pieces together, but the family pet intentionally distracts them just as they are about to have the epiphany.
About Once an Episode for Inspector Gadget, the endearingly inept "world's greatest detective." He'll notice the odd things going on, notice the little man in the coat following him, and completely fail to realize it's his own dog.
Subverted in American Dragon: Jake Long with Professor Rottwood constantly trying to catch the dragon that he keeps seeing and no one else does, but never catches on to the fact that Jake is the dragon despite huge amounts of evidence. At least until a certain episode in Season 2, when he tricks Jake into revealing he's a dragon and reveals that he's had his suspicions for some time.