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.
Setsuna: (beating herself up for her overactive imagination) This isn't a future! This is just a delusion! What's wrong with me! This isn't right! I'm bad! I'm perverted!
Kaede. Her pactio kiss (which she held 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) involves a look◊ that can best be described as predatory.
Kaede: My first kiss...I'm nervous. Negi: You don't look nervous...
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 The Familiar of Zero, 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...
Mai, who works for Pilaf in Dragon Ball. When Pilaf said that they needed to find the "balls", Mai simply responded, "Perhaps between that man's legs." Pilaf and Shu didn't take it well.
Takeo Takakura in Magic User's Club is plagued by his own perverted thoughts, usually directed at his female club members.
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.
Some sketches and lines imply that the super sweet, motherly, tearful and humble farm lady Ukraine...isn't all that modest.
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 ½, 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.
In the Yuri Genre 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 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".
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 example 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.
Natsu switches quite a lot between this and Chaste Hero. He seems to be a chaste hero by default, but when he gets time to think, he isn't all innocent. Firstly, he's the one to suggest that the guys peep on the girls in a hot spring. Later, he is asked how a distressed Lucy is doing. Natsu replies that she is currently showering and asks if he should check up on her again. The others say that he'd better not, and Natsu initially doesn't understand why (completely missing that it's inappropriate to walk in on the opposite sex in the showers). But when he understands their point, he gets excited and tries to run off to see Lucy naked. Lastly, when a naked Lucy is thrown into him, she desperately asks him to not look at her breasts. Natsu's reaction? He covers her breasts with his hands. It's ambiguous whether he did it on purpose to get a feel or if it was an Innocently Insensitive solution (after all, if he covered her up, he couldn't look at her, and she only asked him to stop looking, not to stop touching).
Makise Kurisu of Steins;Gate picks up on Daru's innuendos, which he the points out each time much to her embarrassment.
The hyperactive, flusteryCloudcuckoolander 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...”
Yu Narukami aka the Male Protagonist in Persona 4. 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!" Then, when Shadow Rise appears on Midnight Channel, he keeps pressing the record button without diverting his eyes from the screen, then becomes disappointed upon realizing that the channel cannot be recorded.
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 and thus much easier to target.
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 due to the context, mainly attempting to rape someone, 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 Sakura-sou 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.
Minamo is revealed to be this, thanks to too much alcohol and a poorly timed question from Tomo, prompting her to say "Let me tell you about men" and deliver a long speech on the matter. The speech itself is censored with calming music and relaxing scenery, but given the girls' reactions apparently it was very educational.
Osaka is the only one who doesn't react to the speech with confusion (Chiyo) or embarrassment (everyone else), listening intently and outright telling Chiyo to be quiet when she tries to interrupt.
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'.
"You know, for someone who kept calling me a pervert... you have some very interesting thoughts."
More than one My Little Pony: Friendship Is Magic fanfic has Fluttershy as the author of saucy novels (as being an animal caretaker doesn't pay the bills). One particularly blatant example is Do You Really Want to Know?, in which Twilight Sparkle and Princess Celestia discover a series of miscommunications is due to a draft of one of Fluttershy's stories getting attached to one of Twilight's friendship reports. Celestia immediately wonders why Fluttershy was writing a slashfic involving her and all her friends. With illustrations. Twilight asks if they really want to know, and Celestia replies that no, they really don't. Princess Luna does.
Twilight Sparkle is a frequent recipient of this trope in fanfiction too. Romance Reports for example has Twilight take to researching love and sex with gusto, having very little hesitation to the idea of having sex with the first willing ponies she can find For Science! (which isn't even what she was told, just an idea she made up herself), and at one point casually invents the pony version of the Kinsey scale.
In Thanks Kyubey, Madoka has some interesting thoughts on whether the undead aspect of being a Magical Girl is a curse or a blessing.
Another prevalent idea in fanon is that 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.
Film - Animated
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.
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 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 Harry Potter and the 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 the Discworld, the normally single-entendred Nanny Ogg is rendered speechless when the formerly naïve Magrat Garlick caps her with a perfect double entendre.
"A man with a limp what, Nanny?" (pause) "Look, I am a married woman now, you know!"
Occasional hints are given that Willow is 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?"
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.
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." In Serenityat the very end, when Kaylee and Simon are, well, taking the "unresolved" out of their Unresolved Sexual Tension, River is seen spying on them from above with a curious look on her face. For bonus points, Simon's her brother. 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. And her "cockney come-on" to Badger.
The episode "Amy's Choice" hints the 11th Doctor might be the darker side of this trope.
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!
On a much lighter note, Rory, if the 2011 Red Nose Day short is anything to go by. He responded quite well to the sight of his wifeflirting with herselffrom the future. 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.)
The Tenth Doctor once remarked that a "solid leather" slave drone rather suggested that "someone's got one hell of a fetish."
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. Troy is seen taking notes as she describes her actions.
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).
Star Trek: Voyager. It may be just scientific curiosity, but when Q is about to get it on with a female member of his species, Captain Janeway suggests giving them some privacy.
Q: What's wrong, Kathy? Don't you like to watch? (Janeway looks indignant, then when Q turns to Ms Q sneaks close with an eager expression. The two Q's touch fingers and shiver in delight) Janeway: That was it?!! Q: You had your chance. Don't go crying about it now.
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.
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.
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. She can also be found at one point rummaging around in Shepard's underwear drawer, which occurs with both genders.
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. All those downloads still occur if Shepard is a woman.
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.
Given that Protheans have empathic abilities allowing them to view others memories, Javik has some unique dialogue for a Male Shepard romancing Tali, in which he implies that he might have witnessed a few intimate scenes whilst he read their DNA.
Kaidan Alenko comes off as prudish at first, even turning down the offer of a threesome with FemShep and Liara, but gives a rather infamous response to the mention of how young men were affected by the sight of Liara's mother in a pinstripe suit. ("That does sound like something off an extranet fetish site." (beat) "What?") This is played up even more in the third game.
Of all characters in Fire Emblem Awakening, the very serious and straightlaced Laurent seems to be this. In his and Noire's S support, it look like he's a masochist, expressing excitement over one of his girlfriend-to-be's Split Personality outbursts.
From Tales of Xillia we have Jude edging ever so slowly to Milla before backing away with a blush saying that she looks like a regular woman. There's also Elize, who's living doll moterboats Milla. Elize's doll has no mind of his own. He just voices and acts on Elize's innermost thoughts.
The Duchess in Embric of Wulfhammer's Castle starts off as this, desperately trying to maintain her Proper Lady persona in the face of while all the situations that conspire to rid her of her dress are annoying, some of them are also pretty fun (except for constantly being tied up; she always hates that). Most of the routes have her abandon it though, particularly the ones that have her embrace the "Dark Duchess" persona, while another ending has her get most of the ladies in a Duchess-centric orgy.
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 Danganronpa, at least to "Byakuya-sama." She often mentions him belittling her with a rather...peculiar facial expression...
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.
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.
Questionable Content: Hannelore isn't so much "covert" as she is "severely dysfunctional". Nonetheless, it's played off like this trope when she learns from Marigold what "yaoi" is, or gets caught peeking at Dora's collection of... personal effects.
"I wasn't... I was just... *beat panel* ... how does that one work?"
Mild-mannered gamer geek Dale tested an AI virtual companion service... which dressed the companion as a skimpy Meido based on his internet history. He also apparently owns the entire series of Magical Love Gentlemen (the aforementioned yaoi series Marigold showed to Hannelore).
"Summoning Sweeties", a Whateley Universe story, reveals that the character of Molly is one of these. Pity her girlfriend.
From Phineas and Ferb: While it's not exactly sexual, watching Ferb suddenly purr suggestively or start hitting on Isabella has to be a Funny Moment. Made even funnier because of it's contrast to Phineas and his relationship to Isabella.
In one episode of Metalocalypse, Murderface tries to sound chivalrous and defend women's honor, but his bandmates see it for what it is; a transparent ruse to get women to sleep with him. It doesn't work for him at all.
Finn is usually cheerfully oblivious to romance beyond the very basics of crushes and kissing, but many times he's shown to have fantasies and urges that he might not fully understand himself. This is most apparent in "All the Little People", where Finn is given a bunch of little Simish people resembling his friends and the first thing he does is start putting them in all sorts of relationships, including the Little version of himself with the Little version of Lady Rainicorn (his brother's girlfriend), then Little Finn with both Little Bubblegum and Little Flame Princess (and he blushes when they start fighting over him).
Jake keeps that aspect of his life very private and seems like a childish goofball most of the time, but his speech to Finn in "Burning Low" heavily implies he and Lady Rainicorn have lots of kinky interspecies sex.
Tree Trunks, of all people. She crushed on Finn (fortunately, it never went anywhere) and in "Apple Thief" she slapped one of the Banana Guard's butts.