Ami Mizuno/Mercury in Sailor Moon sometimes has shades of this, with the excuse that she really is the smartest of all the girls. Despite horrible reactions to love letters, she was worldly enough to assume alien-turned-villain Fiore was actually attracted to Usagi's boyfriend. The joke gained more fodder with the introduction of Haruka and Michiru, where Ami is the only character not completely unfazed by the situation and quite frankly understands the nature of their relationship. Similarly, a much later gag from Stars with a handsome young man and a short towel has all the girls shocked... save Ami, who seems to be peeking between her face-covering hands. And let's not forget she's got very exclusive Starlight fan stuff that the other girls (much more open Starlight fangirls) don't...
The otherwise motherly and elegant Cherry in Saber Marionette J fell victim to these, with her embellished daydreams about Otaru becoming increasingly lewd over time, sometimes ending in an ecstatic pile of squee right in front of a very confused and creeped-out Otaru. Hanagata did the same towards Otaru and at least once in Saber Marionette J Again, Luchs did towards Faust.
Not to mention that she held that kiss for a few panels and her reply to Kamo telling her the pactio was complete was "Ohh...is that so" while giving Negi in an obviously deliberate Marshmallow Hell. Negi's hand is also blatantly groping her and the sound effect has a heart next to it. She may be a ninja but this is one area she ain't too subtle in.
Haruki Hanai from School Rumble tries his best to be a very moral and strict character, but he is human with his own perverted moments and thoughts.
Kareha from SHUFFLE!. Only covert in that she doesn't say out loud what she's imagining. However, whenever a situation that could be construed as romantic or perverted presents itself, she will Squee and glow.
Mirei Shizuoka of Umisho is viewed by her peers as being pure, innocent and shy. Yet she wears lingerie that's extremely sexy beneath her clothes, has expressed interest in seeing the bodies of her male team-mates on the swimming team, once suspected Kaname and Amuro of doing This and That, and has expressed interest in buying a large, phallic antique.
Tsuyuri from Doujin Work acts like an emotionless girl most of the time and has a very youthful, sweet appearance. Still, she is one of the most perverted characters around, as evidenced by the extremely sadistic erotic doujinshi she produces. She also projects her fantasies on her friend Najimi, who she firmly believes to be a masochist.
Yoshika from Strike Witches develops a thing for big breasts, probably because she practically becomes surrounded by an amazon brigade consisting of scantily clad, buxom young ladies?her best friend first and foremost. Of course there is nothing wrong with that in and of itself, but Yoshika tends to act on her attraction at the most awkward moments.
Louise of Zero No Tsukaima, especially in the light novels. She beats up Saito at the first sign of his pervertedness, yet whenever we are shown her fantasies, it's rather... saucy. At one point she attacks a large crowd for waking her up from a dream of her and Saito that was "just getting to the good part".
To someone who didn't know better, Yuria of Yuria 100 Shiki would appear to be a Covert Pervert. In fact, she is a Ridiculously Human Robot specifically programmed to be such and one of her features is she will instantly imagine the indecent side of anything.
Tomoyo Dadiouji in Cardcaptor Sakura is calm, mature and refined in most situations, she also has a passion for dressing Sakura, the perpetually oblivious target of her affections, in a vast array of fetish-tastic outfits while she records her... and watching aforementioned recordings repeatedly... alone...
Yukinari of Girls Bravo is rather reluctant to be around girls mostly because of how he's been bullied and beat up by girls his whole life. He also gets incredibly nervous when Lisa, who is infatuated with him, constantly tries to abduct and seduce him. However, he got a nosebleed when he saw Miharu in a blouse and panties, and one episode reveals that he keeps porn under his bed.
In Goshuushou Sama Ninomiya Kun the innocent looking Mayu is actually a Yaoi Fangirl, who writes her own yaoi manga, and Reika can actually be incredibly perverted, which she hides behind a Tsundere facade and hits Shungo if she feels he's acting perverted.
Mafuyu from Seitokai no Ichizon. She has a shy personality and looks innocent but she is a huge yaoi fangirl who fantasizes pairing Ken romantically with a boy named Nakameguro. In fact, when it comes to yaoi, Mafuyu can actually be just as perverted, if not worse, than Ken.
In that case she will first video tape you or take photos, then beat you up
Seto no Hanayome episode 15. When the class president says Nagasumi has become more manly, two flashbacks are shown of him naked.
In Eyeshield 21, when Sena, Monta, Mamori, and Suzuna visit a bath house in order to talk to Kakei of the Kyoshin Poseidons, Mizumachi's attempts at peeping on the girls' side lead to the normally shy and quiet Sena having a vision of Suzuna, naked except for a towel held against her front.
Yuuki Rito of To Love-Ru is one, which a bit of a surprise considering he is Allergic to Love to a small degree. First it began with the few and far between Imagine Spots centered solely around Haruna, before branching out a bit to include others. By Darkness he seems to be strangely fine with the 'Harem Plan' and dreaming of naked girls in the bath.
In Ranma ˝, perverts tend to be more obvious then anything — Happosai and Tatewaki Kuno most prominently. However, there are subtler displays of perversion. UkyoKuonji is normally the most normal-seeming female of the fiancees, with a record that includes slapping Ranma for flashing her breasts to Ryoga and whacking him for calling her cute/asking if she loved him (admittedly, she had been attacking him just before). However, when Genma (in the manga) reveals he has a nude photo of Ranma, Ukyo begs him to let her have it and is shown practically drooling over what she can see of it.
Speaking of Akane, for being such a prudish girl who freaks out at the mere sight of a naked man, she is also the quickest person of the cast to see the perverted potential in just about any whacky set of hijinks. Especially if it involves Ranma. A first-rate example is when Kuno was about to ask for a wish to a magical rock: while she and Ranma discussed it, Akane imagined Kuno asking for female!Ranma to love him, and immediately came up with the Imagine Spot of Kuno taking advantage of this to rape Ranko on the spot. She ends up giving a Big "NO!".
Sui-Feng. Holy SHIT, Sui-Feng. Who'd say that the coldest, more ruthless Tsundere in the Gotei is sucha Yoruichi fangirl? Not to mention there's how, in an omake, she pinned Ukitake to a tree with kunai so people could take photos of him.
When Ichigo tells Rangiku she can't stay at his place, she lets her skirt ride up and begins unbuttoning her blouse. Ichigo slaps his hands over his eyes and protests aggressively, telling her off... while all the time peeking at her body through his partially opened fingers.
Aizen can measure your bust, waist, and thigh sizes with his eyes. Enough said.
In the Girls Love manga Husky and Medley, Medley is surprised to learn during an after-school encounter in an empty classroom that Husky, who everyone thinks of as the perfect strait-laced schoolgirl, actually has a bit of a dominance kink. After Husky holds Medley up against a wall in an embarrassing position while kissing her, Medley reports to 2ch that "this was the day I became a masochist".
Mio in Nichijou has moments of this. Throughout the episodes, she has to chase down her friend Yuko to get back her notebook after belatedly remembering she had drawn a naughty picture of the guy she likes in it, she gets in a drawing competition with Yuko and ends up getting carried away. Most recently she ends up attacking a police officer, an old man, Yuko, and a goat when they all catch sight of her drawings in her desperation to get them back.
Ebisu in is also a major example of this. He always berates Naruto for using his Sexy no Jutsu technique (calling it indecent) but is nonetheless consistently "defeated" by it. Naruto even refers to him as a "closet perv".
Sakura is another example. When Konohamaru showed off how he had learned the Sexy no Jutsu, Sakura got angry and called him out... but then he showed his "counterattack" by creating a Ho Yay Sexy no Jutsu with naked Sasuke and Sai. Sakurapromptlyhad a nosebleed.
Fairy Tail has actually several examples of this. The most prominent would definitely be Erza with all her weird, often quite Stripperiffic armors, of which she states she prefers the Bunny Girl. Later, she buys a "seduction armor" which is essentially several types of Fetish Fuel packed into one piece of clothing. In the Fairy Hills omake, Levy also mentions that she apparently likes "sexy books", and when Natsu and Gray looks through Lucy's chest of drawers to find her underwear, they easily make an interested Erza join them.
Happy has one single and very small, but quite noteworthy here. While Lucy and aforementioned Erza defeat most of their opponents in the panel in the middle row with normal attacks, Happy apparently defeats his by ripping off his clothes on the lower body.
Makise Kurisu of Steins;Gate picks up on Daru's innuendos, which he the points out each time much to her embarrassment.
The hyperactive, flusteryCloud Cuckoo Lander Oshiroi from Ben-To. When Satou asks her if she wants to join the Dogs, she thinks he wants to know if she wants to get gangbanged. She doesn't reject the idea outright, just says she'd prefer her first time to be one-on-one.
Mizuki Himeji from Baka To Test To Shoukanjuu certainly qualifies, during an event were the summoned being spoke the characters true feelings Himeji's confesed to have thought "weird thing" when the other were talking about ecchi things.
Also this from volume 7 of the novel:
Mizuki: I think Minami-chan will use this chance to touch Akihisa-kun's chest and butt...that's too sneaky...”
Minami: Wh, what are you saying, Mizuki! How can I do such a thing—eh, what? What did you just say? Touching...Mizuki, what were you talking about...”
Minami: Mizuki..what were you planning to do to Aki...”
Yuu Narukami aka the Male Protagonist in Persona 4 The Animation. In the original game this was more optional since you, as the player, got to choose whether he was a pervert or not; in the anime, however, Narukami makes this face◊ upon seeing Shadow Yukiko in the Midnight Channel, and then says "I wish I had taped it." And later, when Shadow Kanji and his minions have Yukiko and Chie covered in slime, Yosuke asks him if he does have a camera, and he says "Dammit, no!"
Because Yu is also The Stoic, he almost always gets away with making perverted quips around his female friends, unlike Yosuke who tends to be a lot more energetic.
Momoka Nishizawa from Keroro Gunso may be one. When Mois gets "scary story" (kuaidan) mixed up with "dirty story" (waidan) in one chapter, Fuyuki and Natsumi listen to her story red-faced, too embarrassed to comment. Momoka's blushing too, but is also listening intently, and even tells her "Yes, yes, go on!" In another chapter, Momoka tries to get Fuyuki to indulge in some Intimate Healing, much to the delight of her "dark side".
Dark!Momoka: This isn't just a confession... you're gonna skip straight to @#$%! Go, Momoka!
One of the few times when this is NOT Played for Laughs is Yuri Tokikago from Mawaru-Penguindrum. Before episode 15, who would guess that Yuri would know how to tie someone up in shibari bondage? Or have access to what're essentially roofies?
Hadzuki from Ojamajo Doremi gets a moment during the Fathers' Day episode of Dokkan!: While Hadzuki, Aiko, and Momoko are helping out at a bathhouse their classmate's family owns, Kotake comes in and strips down without noticing Hadzuki there helping a toddler. After Aiko bursts in to see what the commotion is all about, Kotake storms out in an embarrassed panic, leading to the following exchange:
Aiko: Why is he getting so embarrassed? And now he's going home without taking a bath?
Nanami in Sakurasou No Pet Na Kanojo may look relatively normal (if not a bit workaholic), but she owns some rather fancy underwear, and her usual reaction whenever confronted by a strange situation is to assume the most perverted possibility.
During the Chunin Exams, Hinata was sitting next to Naruto in A Growing Affection. it turns out she tried looking at his test to check on him but because he kept fidgeting she caught a glimpse of...something else.
Naruto becomes this in Escape from under the Hokage's hat. Due in part to having had a seal placed on him (multiple actually but just explaining this one is important for now) that screwed with his libido and hormones but was removed forcing the 13 year old to just deal with the overload. Naruto then travels in a group with Hinata, Shizune and Tsunade. Cue Naruto suddenly thinking about how bad he wants a backrub from Shizune, wants a hug (Marshmallow Hell) from Tsunade, comments on how he wants to "hold Hinata and never let her go" and suddenly be turned on by Hinata's laugh.
Speaking of Hinata, she also gets this a lot in fanfiction.
Nagato and Hanyuu are this in Kyon: Big Damn Hero, spending part of the time when they were watching Kyon 'enjoying the view'.
Sunny Breeze in Racer And The Geek behaves like this, although he adamantly denies having any sort of sexual feelings or attraction. It's definitely not the case.
In The Second Try Shinji is peacefully watching Asuka breastfeed their child. She sees him looking at her and asks if he's jealous and wants a taste (Character Development, a resolving of their UST and marriage and a child with Shinji has made her stop being a Tsundere). Shinji said it best:
"You know, for someone who kept calling me a pervert... you have some very interesting thoughts."
Michelle in the first American Pie film, who comes off as dorky and awkward until the Wham Line that shows that she most definitely isn't.
In the S Club 7 movie Seeing Double the band kidnap their dim-witted clones and tie them up. The Rachel clone wonders if it's part of their training program and asks "Do I tie you up now, Bradley?". Bradley gets quite hot under the collar and says "we'll talk about it later".
Later on in the film we find out that the clones are taught to shower together to save water so the fun starts when Bradley is showering in the garden and the Rachel and Hannah clones climb in with him. He heads for the hills when the Jon clone climbs in too but Tina sneaks a peek at them.
In the book Behaving Bradley, a high school boy gets nicknamed "Microdick" after the other boys see him putting his bathing suit on in the locker room. Hopie, a sweet, naive girl, asks the main character what the nickname means, and he tells her it's because the boy wants to be a disc jockey and use a microphone. She responds "Oh, I thought it was something about his penis."
As revealed in Goblet of Fire, Moaning Myrtle "sometimes" sneaks into the prefects' bathroom to watch them bathe. Harry finds this out while taking a bath himself to figure out a tournament clue that's only comprehensible underwater.
In Buffy the Vampire Slayer, occasional hints are given that Willow is actually one, like her "Everyone's getting spanked but me." comment (and the accidental ogling of Dawn (the Dawn part was the accident, not the ogling) that one time).
"Oh, right. Me and Oz play "Mistress Of Pain" every night"
"Did anyone else go to a scary visual place?"
She suggests that Buffy might become a transsexual after being infected by a demon (she would get an "aspect of the demon"). "Was it a boy demon?"
Her girlfriend Tara seems to be the same.
Buffy's no slouch either. She's the aggressor in each of her relationships, she's into femdom if Spike is anything to go by, in the series finale she said he and Angel might do oil wrestling and the comics...the comics has her missing the sex before her deepest fantasy is revealed. That fantasy is her playing mistress chained to a naked Angel and Spike, wearing a Naughty Nurse Outfit. It's been a slow year.
This is the most obvious character trait of Tobias from Arrested Development, who never seems to consciously think or care about sex at all.
There's a rather startling scene in Pushing Daisies where Chuck, in an attempt to prove that she's not as sheltered as she seems, talks about her aunt's collection of erotica.
Mindy from Mork and Mindy. In the pilot, she asks Mork to test his voice by reading from a book she has. Turns out it's a steamy romance novel. And later in the series when it's revealed that Orkan ears unscrew, she says "Gee, I'm afraid of what else comes off!".
Phoebe from Friends was initially like this before they used it so much that it became less covert and more just part of her character that she was the kinky, frequently sharp tongued and kind of mean, one.
The iCarly trio want to hire an intern to help run their show. Sam wants to know if the intern will scrub her when she's having a shower or bath.
Rachel and Emma from Glee. "Push it" was Rachel's idea and Emma informs Rachel that someday not having a gag reflex will be a gift. If you know what she means.
Though Firefly has plenty of characters with overt sexuality, the last place one would expect to see such sexual commentary from is the somewhat unhinged yet innocent River. Nonetheless, she gets in the occasional comment that makes it very clear she's paying attention.
In the comic Those Left Behind, Wash and Zoe make love on the bridge, and then suddenly have to call everyone else up to the bridge when they find something important. No one says anything as the two are straightening out their clothes... until River blurts out "It stinks like sex in here."
Not to mention in Serenityat the very end, when Kaylee and Simon are, well, taking the "unresolved" out of their UST, River is seen spying on them from above with a curious look on her face. For bonus points, Simon's her brother.
And her "cockney come-on" to Badger.
River doesn't hesitate to bait Jayne into chatting about his "man-parts" - and it doesn't seem to bother her when he does, either.
Also, the reason everything went wrong in that episode was Amy's fault. Rory was helping the Doctor fix the TARDIS and Amy was wearing a skirt. On a glass floor. Under which was Rory. Rory did apologize, for what it's worth (for dropping whatever he was holding, not for peeking.)
And Amy owned up immediately to being the ultimate cause, no less.
Amy Pond, who doesn't turn away when the Doctor decides to change his clothes in front of her. Twice.
The Tenth Doctor once remarked that a "solid leather" slave drone rather suggested that "someone's got one hell of a fetish."
In "The Angels Take Manhattan", the Doctor is reading a trashy detective novel. He doesn't seem to be entirely aware that he's reading it out loud and saying "yowza!" to the descriptions of the Femme Fatale detective's impressive cleavage. Later in the episode, it's mentioned that he has "the face of a twelve-year-old".
Becomes funnier after the reveal that the Femme Fatale is actually River. Who is his wife!
Many instances of Annie on Community doing this. Most noticeably in her stint as Hector the Well Endowed, a D & D chracter, who has to seduce a elf maiden.
Dr Chi Park on House. Comes across as mousey and repressed, 95 per cent of the time. The other five per cent she's accusing Dr Adams of wanting to masturbate over her, or casually claiming to have had sex with over thirty guys (which she then admits is a lie; whether the true figure is higher or lower remains unknown).
In The Moon is Blue, Patty O'Neill insists on having people respect the fact of her virginity, but talks about sex enough that they call her out on it.
A rare non-comedic example of this trope is James in Silent Hill 2, who initially appears to be a relatively normal (if rather dense and insensitive) individual until it's revealed the majority of the twisted abominations that have been attacking him over the course of the game are the personifications of his sexual repression.
To give the man some credit, this is Silent Hill! This place gives form to a persons inner conflicts in the most bizarre ways imaginable. While the creatures in the game have a clear sexual theme, there's no indication that he's particularly unusual.
Taokaka of Blazblue is a childish, innocent-seeming catgirl who's mostly interested in helping her village and eating — she even sometimes calls characters by cute, childish nicknames, like referring to Nu-13 as the "flappy thing" and Litchi as "Boobie Lady". Except that it later becomes obvious from further dialogue that "Boobie Lady" is not simply a cute nickname based on one two of Litchi's distinguishing features, but that she's downright obsessed with breasts in a seemingly fetishistic way... as seen at one point with the poor 'Average' Tsubaki.
Diving deep into the heroines' Cosmos Spheres in the Ar tonelico series reveals their "true" personalities, thoughts, and desires under the masks of being pure, shy, cute, bossy, hotheaded, or whatever in the real world. Given how they present the games, Those heroines have... a lot of unhealthy suggestive things in their minds.
The first game gives us Aurica who is normally very soft spoken and unsure of herself. In the latter half of her Cosmosphere, she kidnaps Lyner, ties him to the bed, straddles him and electrocutes him when he tries to run, all while wearing nothing more than a towel.
Apparently this is so dangerous that An incarnation of the good in Aurica's mind appears to save Lyner and that level of the Cosmosphere is entirely abandoned with dangerous consequences later.
Also MOST suprisingly Ken! In the original Japanese version he's not above using the fact that the Female Protagonist is Shotaconagainst her. But similar to Akihiko's, it's when he goes to your room a second time.
From Persona 4, Yukiko Amagi. Normally rather shy and reserved, not to mention the low tolerance she has for what she perceives as, in her somewhat ditzy mindset, lecherous behavior. Once she gets drunk, however, or at least believes she does, her inhibitions fly out of the window. Also, if you are in a relationship with her, she's more than happy to dress up in one of the sexier alternative costumes. She would prefer it to be in private, though, instead of in front of the whole group.
Kenzie Kensington of Saints Row is a not so covert example. When discussing a BDSM club she mentions the safe word she uses there, her crib includes a leather mask and giant Penetrator dildo, and her reply to needing to get laid is that she uses electronics instead.
At one point in Kid Icarus: Uprising, Palutena mentions she could read Pit's mind, telling him he'd better not be thinking anything naughty. Pit seems rather defensive and quick to react, even giving a Suspiciously Specific Denial when Palutena tells him it was a joke.
There is a hot springs scene where (in the Japanese version anyway) she practically begs Pit to take off his clothes.
Kasumi Goto of Mass Effect 2 uses her cloaking skills to watch Jacob, and hints at watching Shepard with his\her love interest. During the actual, well, scene, given how accurate her comments are. Taken to truly Up to Eleven levels in the Citadel DLC where she is a classier mix of Matriarch Aethyta and Mel the "Infiltrator Tits, imagine the kinkiest thing you can and hang a Hanar off it" marine.
Also in Mass Effect 2, Shepard's shy Quarian friend from the first game, Tali'Zorah, is shown in the Shadow Broker's files to have installed a certain nerve-stimulation program into her environment suit several times, eventually settling on the deluxe edition right after downloading an educational video about human courtship and mating. As Tali is a romance option for male Shepard and has a massive crush on him, one can assume that he is the reason for these activities.
In Mass Effect 3, there are hints that the shy and socially awkward Samantha Traynor is this, for example when she boldly attempts to seduce a female Shepard when given the chance. The Citadel DLC takes away all doubts, revealing that she fantasizes about EDI—or at least her voice—and she shows interest in EDI's list of extranet sites that basically amount to lesbian organic on synthetic porn.
Also the Normandy's helmsman Jeff "Joker" Moreau, who enjoins Shepard to "take pictures" when Jack and Miranda have their dustup in 2 and can't stop staring once EDI acquires a body in 3. He's also noted by EDI to have a rather sizable Porn Stash; in particular she claims that most of the seven zettabytes of porn she uploaded to Cerberus' servers as a prank after leaving Cerberus belonged to Joker. (She may be have been joking.) Naturally the Rule 34 people take this and run with it, including having Joker peeping on Shepard and his/her love interest with the Normandy's security systems.
Little Busters has Nishizono Mio, who, upon being invited by Riki to be the manager for their baseball team, more than happily fills in the blanks with her mind when Riki fails to mention the "baseball" part quickly enough. Then there's the part where she sees Riki and Kyousuke acting very touchy and mistakes them for gay. Or later when she presses him for information about their childhood together and sighs dreamily... It's not just yaoi, either - one of her sayings after being given a nickname for losing a battle is "Is this some kind of SM thing? You have strange fetishes..."
Touko Futawa from Dangan Ronpa definitely appears to be a great example of this trope, at least to "Byakuya-sama." She often mentions him belittling her with a rather...peculiar facial expression...
A rare male example: Onii-chan from Tsunami Channel has shown hints of secretly being a little more "hentai" than he usually acts.
Alex/Murfs of Khaos Komix always blushes around his love interest Tom. In the other characters' stories, the impression is that he's blushing because he's shy and embarrassed about his attraction to Tom. In Alex's own story, however, it's revealed that his constant blushing is due to the incredibly dirty thoughts he has about what exactly he'd like to do with Tom.
Justin, of El Goonish Shive, of all the main characters, is the first to wonder if using a Transformation gun on a female results in a male form with generous... er... gentlemanly parts. He was gender-bent at the time, but it was still unexpected.
Rather prevalent in Touhou fanon is the idea the Koakuma is a succubus. Bound in servitude to Patchouli and made to act as a librarian. The jury's out on which is the bigger pervert.
Established very early in Danny Phantom. Danny and Tucker are perverted. We have them getting near the girl's locker room, Danny getting beaten up for trying to meet girls that way (Bad idea), Tucker placing garbage near the girl's locker room, even in season two we see Danny coming out of the girl's locker room, etc.
Lois Griffin from Family Guy. This woman seems to have done pretty much anything.
The Hunchback of Notre Dame: Judge Claude Frollo might qualify as this, given how he hides his lustful thoughts behind a self-righteous demeanor. He might alternatively qualify as a subversion, though, given how Esmeralda sees right through him. Consider the scene where he sniffs her hair.
Esmeralda: What are you doing?
Frollo: I was just imagining a rope around that beautiful neck.
Esmeralda: I know what you're imagining.
Frollo: ... such a clever witch. So typical of your kind to twist the truth, to cloud the mind with unholy thoughts.