Angel Sanctuary features a romantic relationship between the main character, Setsuna, and his (real, not adopted, foster or step-) sister Sara. Rosiel wanted this with Alexiel, but she wasn't having any of it. Setsuna and Sara's relationship is even relevant to the plot. In fact, it's what drives the story.
ALL the angels are related, so any Angelic couples are technically incest, like Zaphikiel and Anael, Lailah and Niddhegg, Raphael and... well, a lot of others with Raphael.
In an unusually negative scene, there is a pseudo-incestuous rape sequence in Ayashi no Ceres. It also contains a subversion and plot device of this trope, seeing as Shisou Mikage, who is still madly in love with his wife Ceres, is reincarnated as Aki Mikage. Aki's twin sister Aya is the reincarnation of Ceres, and she is eventually led to kill him to save both herself and Ceres. Aki and Aya themselves do love each other greatly, but not in an incestuous way.
Hansel and Gretel from Black Lagoon, even though it's not clear which of them is which, or if they're even different genders.
Averted in Fist of the North Star when Juuza discovers his childhood sweetheart Yuria is actually his half-sister. They drift apart soon after, having never consummated their relationship.
Genshiken pokes fun at this, with Sasahara, who actually has a sister, delivering the quote from the main page.
Massively implied in .hack//tasogare no udewa densetsu (especially in the anime, where it's played mostly straight, more so than the manga, where it's largely played for laughs) between protagonists Shugo and Rena that the series has become derisively known among critics as ".hack//Twincest".
Koi Kaze plays this trope straight with two blood siblings who haven't seen each other since childhood.
Delphine from Last Exile has a similar fascination with her brother Dio.
And Dio fears her to death, with good reason — the gal's completely crazy, and not in a good way.
Magikano plays with the trope: The main character's oldest sister has a downright obsessive love for him (one that is definitely not simply sisterly) even to the point where she claims she will marry him and becomes ultra possessive whenever any other girl shows any interest. However he doesn't seem to have any interest in her. The arrival of the protagonist's Magical Girlfriend makes her intensely jealous and always vying for his attention.
Despite the show's fanservicey roots, it's never portrayed as actually romantic or sexual though. The manga on the other hand...
In Marmalade Boy, Yuu and Miki become step-siblings when their parents marry (with both sets of parents splitting up and marrying each other), and then find themselves growing attracted to each other.Later in the series, they find evidence that they may be actually blood siblings; before they learn that this was all a big misunderstanding (said evidence wasn't referring to Yuu but to his mom's still-born child, who would've been his older sibling), they decide that they would marry regardless with the understanding that they will never have children.
Interestingly, the Mangaka (according to her notes on the series) originally planned for them to discover that they were blood siblings and split up for good, eventually hitching up with their unrequited love interests in a Distant Finale. Her producer convinced her that it wouldn't go down well with the fans...
In Maze Megaburst Space, not only is the central couple a pair of blood siblings, and not only is the central plot their successful and unrepentant plot to be together, but it goes even beyond that...
Onegai Twins has what may or may not be an incestuous Love Triangle, between a boy and two girls who both claim to be his twin sister. To add to the blurring of the line, the girl who turns out to actually be his twin is different between the anime and the novelization. Interestingly, though, the setup of the plot clearly steers away from this: whoever turns out to be the twin must step out.
That said, both girls kiss Maiku before it's over, so be ready for some Squick. The possibility of being his sister keeps them from getting really aggressive, but that's all it does; their ambitions are not deterred.
Meanwhile, perhaps to provide contrast, there's a minor character (Matagu) who's blatantly attracted to his little sister Haruko.
And Haruko doesn't quite reciprocate, but at least clearly knows and doesn't mind. After describing his use of The Hands On Method, we get this:
Haruko's friends, in unison: "Your brother's a pervert!"
Haruko, cheerfully: "He is!"
The attraction in this series isn't all that unrealistic. The Westermarck Effect isn't in play, since the twins were separated at a very young age (maybe 2 at the latest), and the general principle of genetic attraction makes it unsurprising that the sister would have some feelings upon seeing someone who may (not) be her brother. That the other is a childhood friend makes it all the more probable, since they would have subconscious affection for one another at the outset. That being said, if kissing somehow Squicks you (the convent just called...), there is some of that and some hand-holding/hugging between the would-be sister and the brother. Otherwise, this is an Averted Trope, since, as stated, the twin is not allowed to continue the relationship (which is part of the drama: which girl has to give up her romantic affections, and which girl gets to be by his side albeit as a sister, not a lover).
Maiku does have a hard time not having sex with either of them in the Beach Episode (complete with imagining them naked, though admitedly chibified) and has to resort to leaving the room to contain his libido. Knowing one is definitely his sister doesn't stop him from wanting them BOTH.
In Revolutionary Girl Utena, not only does Touga's sister Nanami harbor an intense crush on her older brother, but she also has a near-insane jealousy of anyone or anything that might attract more of his attention and love than she does. There is also the strange love-hate relationship between Kozue Kaoru and her twin brother Miki, best displayed in the bizarre bathtub-and-straight-razor scene from the Utena movie. Most important to the plot, though, is the semi-consensual relationship between Anthy and her manipulative and domineering brother Akio.
Ali and En in the anime-only "Makaiju" ("Doom Tree") arc of Sailor Moon. This is explainable to an extent, however: not only are they the only surviving members of their species, but they are "children" of a tree, which used what remained of its powers to "grow" them after the rest of the species was destroyed in warfare; thus making them "siblings" in roughly the same sense as Adam and Eve.
Lampshaded once by Makoto, when "Natsumi" bitches "Seijuurou" out for letting Mako offer him a part of her lunch. She's squicked and says something by the lines of "Wow... these siblings! So weird!"
DiC, perhaps in a result of bowdlerise, had Crimson Rubeus refer to his four main female minions as sisters. He may have referred to their name, Phantom Sisters, but it calls into suspect when you realize most of them are attracted to him.
Saint Beast: Definitely played with in Kira and Maya, particularly in the official art.
Tiriel and Sorath in Shakugan no Shana have an incestuous relationship, though in this case it's portrayed in a creepy light. What theyare muddles the water, but only somewhat. Shana seems to take more offense at the French kissing than anything else.
Alti in Simoun is obsessed with her sister Kaimu, and tries to prod her into choosing to be female so that Alti can become male and "protect" her.
They also have sex once during the course of the show (long story) and in the Distant Finale they are living together even though they both chose to remain female.
Sister Princess and its "sequel" series, Sister Princess Repure, both have incestuous subtexts, but the subtext surfaces clearly in Repure: in the very first episode, Karen recounts how she decided that she would be her brother's bride, despite society's disapproval of such a thing. In the original series it is less visible, although still present — one sister (Chikage) was Wataru's lover in a previous life, Sakuya openly flirts with him (Rin Rin and Mamoru are more subtle hiding their flirting under the disguise of admiration for their Brother), and all twelve spend one episode making mock wedding dresses so they can play at being his "bride".
In The SoulTaker, Runa wanted to marry her twin brother Kyōsuke, who declined the honor.
Ren and Mihato in They Are My Noble Masters have a mutual brocon-siscon relationship, and are quite supportive of each other. It's almost sweet if one is willing to look past the sibling thing. Then again, this is a show that's filled to the brim with fetishes. They do have a route together in the original h-game.
In the same series, Shinra is very open about her sexual attraction towards Miyu, her younger sister. Worse, she sexually assaults her on numerous occasions, which is played entirely for laughs. That Miyu seems to be very ambiguous about this and that the youngest sister is actually jealous for being left out just adds to the squick-factor. Fetishes, indeed.
In Tsukihime, Shiki's sister has a very possessive crush on him. Parodied in numerous doujinshis and official omakes, including one where Ciel points out the hopelessness of the crush. Shiki's feelings are purely platonic. And a large part sheer terror—Akiha is tsundere at best and yandere at worst. Of course, they areNot Blood Siblings, and Akiha does have her own path in the Visual Novel.
Though they never did anything incestuous, SHIKI hints many times that he has romantic interest in his sister Akiha. Too bad all she thinks about is her other "brother," making this trouper really feel bad for SHIKI.
On that note, Azaka from Kara no Kyoukai, who can be considered prototype of Akiha above, also loves her brother deeply, to point where it gets in the way of her becoming friends with the series heroine Ryogi Shiki. Her love may not be the same in nature as Akiha's but since she and her brother were used as a strong basis for Akiha and Shiki, it is likely that the "love for my brother" was carried over as well.
The Spiral manga has a variation: Ayumu was in love with his sister-in-law even before his brother married her, and lived with her after he disappeared. Also, since all of the Blade Children have the same father, Kousuke and Ryoko's relationship, despite growing up as childhood friends rather than siblings, is incestuous. Kousuke specifically asks Ryoko not to call him 'big brother,' saying that he wants to be able to dream of being with her.
All but expressly stated in Edens Bowy between tragic siblings Wietoo and Hairra. Initially averted when Hairra actually tried to pair her older brother Wietoo together with her best friend Fennis in an effort to repress her own incestuous feelings, but it failed anyway due to irreconcilable differences of ideology between Wietoo and Fennis, who also noticed Hairra's disturbingly excessive attachment to her sibling. Eventually the siblings get together when Hairra decides to acknowledge her feelings upon realizing that no one would love her brother as much as she did (which led to a falling-out with Fennis) and Wietoo also realizing that only Hairra would ever accept all of him, including his controversial views on the creation of sentient A.I. Hairra is soon killed tragically sometime afterwards when Wietoo's first android goes berzerk, and she is reborn as his personal gynoid weapon/bodyguard. Later, when they are both killed at the series end, they are reborn together as sentient programs together roaming forever their world's version of the internet.
Aono in Sola is obsessed with her (younger, for a change) brother Yorito to the point of creating a copy of him that took enough power to leave her bed-ridden for years.
It is heavily implied in Narutaru that the bully Aki Honda and her older brother Yasuhito have a ... rather intense relationship.
It's downright spelled in the manga. So much that Aki is once shown straddling Yasuhito while practically naked. Then, Oni shows up, kills Yasuhito by smashing his head on ther wall, and rapes and kills Aki as revenge for what they did to his master, Hiroko.
Said scene is censored in many countries in the world (even the japanese version got censored retroactively) and spelled the end of the series' publication in many others.
Renhou and his sister Miiru in Fushigi Yuugi. In fact, their incestuous relationship got them killed by their people, and they go to the Big Bad Tenkou in hopes he'll help them stay together.
In the first episode of the Voltage Fighter Gowcaizer OVA, the Villains Of The Week were an incestuous set of twins (who were empowered by the Big Bad to save the dying sister) who merged into a gestalt monster "powered by love".
Infinite Ryvius: We eventually discover that Ikumi had fallen in (that kind of) love with his dead older sister
Kanan is Hakkai's older sister in the Saiyuki manga, although this was edited out of the anime version, and, as they had been Separated at Birth or very close to it, they weren't originally aware of it. A tie-in novel also suggested that they might be twins as well, which was approved by Word of God.
She seemed more annoyed at his using accompanying Nanoha to visit Suzuka as an excuse to see Shinobu, given that he doesn't seem completely open about his relationship (In A's episode 9, she teases him about being able to work with Shinobu for Christmas with a cute smile on her face). Interestingly enough, Miyuki calls him "Kyou-chan" (like she did in Triangle Heart) instead of "Onii-chan", like Nanoha does, which may indicate that they're Not Blood Siblings.
In True Tears what starts as a case of Big Brother Instinct evolves into borderline incest when we learn that Jun has romantic feelings toward Noe, his younger sister. This trope is also averted at one point Shinchiro and Hiromi are under the impression that they are siblings but it turns out that they are not related.
Hoshina Utau from Shugo Chara!loves the resident bishonen catboy of the series, Tsukiyomi Ikuto. The thing is, her real family name is Tsukiyomi and she is Ikuto's sister, which does explain why Ikuto is so cold towards her advances — in fact, he's downright disgusted when she kisses him.
The secret of the Kuhouin family in Kure-nai is that each girl born into the family is imprisoned in the "Inner Sanctuary" for their entire lives, for the sole purpose of bearing the children of their brothers to continue the lineage. Their very existence is kept hidden from the public, and the male members of the family marry women from outside the family just to keep up the masquerade.
In Ghost Hound, the main character, Tarou, has a slight obsession with his sister which leads to him accusing the girl he likes of being his sister reincarnated as an explanation for why he thinks about her all the time.
In D.Gray-Man, Komui's attitude toward his sister Lenalee straddles the line between Big Brother Instinct and this trope; even the other characters find it a little creepy and frequently remark on his obsession.
Candy Boy's main theme is the yuri subtext between (fraternal) twin sisters. The lyrics in the recap video appended to the first episode proclaim that "this may be the best pairing in the history of the world". Ahem.
Vampire Knight: Yuki, Kaname's adopted sister, becomes involved in a romantic relationship with him; this wouldn't normally count, except for The Reveal that they are biologically related and this doesn't stop the romance.
Berserk subverts this somewhat, since Serpico and Farnese were in love at one point and are half-siblings, but Serpico's love becomes more brotherly after he learns that Farnese is his half sister.
Minato and Juunichi's relationship in Akane-iro ni Somaru Sakais seen as this by everyone despite the siblings' insistence that it's not. It turns out everyone else was spot on, because when the show ends, Minato is the one who ends up winning. Interestingly enough, the level of incest between Minato and Juunichi changes depending on the version of the story. They're fully blood-related in the original PC game, but Minato is adopted in the PS2 version and possibly in the anime as well.
In Mahou Shounen Majorian, Mari falls in love with the magical girl form of her brother, Masaru—which makes it kind of hard to classify.
Axis Powers Hetalia has both the traditional brother/sister version and a Ho Yay one. On a hand, the Yandere Belarus would love to marry her older brother Russia (also a Yandere), which freaks him out no end. On the other, the Annoying Younger Sibling South Korea isn't much more successful in getting his older brother China (and sometimes his other older brother, Japan), to acknowledge his more-than-brotherly affection. Both cases are played for laughs.
Switzerland and Liechtenstein, while Not Blood Siblings are shown in-canon to be very close, leading to some Ship Tease. It probably doesn't help that they also act like a young married couple at times rather than as brother and sister.
At one point in the Ah! My Goddess manga, a botched love potion fed to Keiichi causes any female to meet his eyes to become passionately infatuated with him — starting with his sister Megumi. She says, "Our love can transcend these foolish bonds of blood!" His horrified reaction: "Oh no it can't!" Fortunately, neutralizing the potion wipes her memory of the incident.
The anime-remade episode has this too, and is more outrageous, where Megumi goes to the length of clinging onto Keichii and fighting over him with Skuld, Urd and Peorth who also fell victim to the effect of the potion.
In Minami-ke, Chiaki and Kana's adoration of Haruka many times looks extreme, the fact that they talk about her possessively and will scrutinize any potential love interest says something.
in Kare Kano, Kazuma and Tsubasa simutanously get crushes on their other as their parents get married. Cue Squick from parents, Wangst from Kazuma which make him run away from home, which makes poor Tsubasa down the mental road before it gets better.
Somethinged in Fresh Pretty Cure!. Miki's brother Kazuki lives with her father (her parents are separated, presumably divorced) and uses his name. She hasn't told her best friends they they're related, and in the first episode she refers to their upcoming outing as a date. The second episode focuses on one of their dates; it also features The Reveal that they're related, but you'd be forgiven for missing this detail. Eventually it's revealed that, when her friends assumed Kazuki was Miki's boyfriend, Miki went out of her way not to correct them because she thought it was cute.
Considering the yuri subtext in the Pretty Cure franchise in general, we have the only Precure-sisters Love and Setsuna from the same series. They are step-sisters, though.
Happy World: The explanation Takeshi uses to explain Elle's connection to him is that she's his step-sister. Cut to Takeshi exclaiming loudly to her in a classroom "We should make a baby." And they actually go halfway through the act before realising that they're not emotionally ready for it.
As it turns out, their relationship to eachother is technically step-siblings... probably. Takeshi's mother is Elle's mother, but Elle doesn't have a father, so it's a bit complicated.
Their child, Prayer, is eventually born... but not through normal means. Takeshi and Elle fuse their bodies, and Prayer is born when they split apart again.
Oniichan Control has the brother who fled from his younger sister because he's developed inappropriate feelings for her. Unfortunately, his younger sister is not only fully aware of these feelings, but returns them in a big way. And she's a first-rate manipulator beneath her cutesy facade, managing to track him down, get admission to the same college he goes to, and worm her way into becoming his roommate. This goes so far that she's willing to stab a girl she thought was interestedin her brother. The entire series is about the brother trying to avoid this trope while the sister tries to invoke it.
Two examples of this, running in both directions, are present in Hatsukoi Limited. Ayumi's brother, Yuuji, is a definite siscon, and Koyoi Bessho is defined by her brother complex. Of course, they are but one small part of the Love Dodecahedron that permeates the series.
In the spinoff of Genshiken, Kujibiki Unbalance has the main character's sister pursuing him endlessly, even going so far as to try perfume that is actually a love potion to seduce him. Instead she just succeeds in getting MC's best friend to kiss MC much to his sister's despair and anger.
An example also occurs in Yuu Watase's pre-Fushigi Yuugi manga, Shishunki Miman Okotowari. Asuka Higuchi falls for her half-brother Manato Sudou early on in the story, and he eventually comes to reciprocate. And then they learn that they aren't blood-related after all—in a very mind-twisting way.
In Shinkon Gattai Godannar!!, English pilot Knight Valentine will flirt with any female in sight, much to the consternation of Ellis, his sister and partner, who thinks he doesn't notice her. But if the way he looks at her swimsuit-clad form and the fact that he sees Ellis' face when an amnesiac Mila is hitting him with Charm Person are any indication, he does notice her in that way.
This issue is addressed in episode 9 of the second season of Hell Girl. The incestual love in this case is one-sided, and the offending sibling is, of course, sent to hell. The episode ends on a lighter note; the aforementioned sibling is not tortured on the ferry (unlike sinners who have done worse), and there is the knowledge that the brother and sister will eventually be reunited as per the terms of the curse.
In Queen's Blade, Elina is quite obsessed with sleeping with her sister Leina, showing flat out disappointment that she couldn't spend the night in her room in the first episode. Leina is more than aware of her sister's blatant lesbian crush on her, which is part of the reson she ran away from home and doesn't intend to return. Though she indulges Elina on occasion, such as episode 9, where she bathed with Elina and spent the night spooning with her, while both were in the nude.
It's actually implied in the main series that Claudette is in love with Elina, but her feelings are unrequited due to Elina being in love with Leina. In the "Hide & Seek" continuity, however, it turns out Elina does reciprocate, she's just more attracted to Leina.
Kiss x Sis is about the ongoing incestuous affair between Keita and his older twin sisters, Ako and Riko, who take turns waking up him up each morning by making out with him beneath the covers, before breakfast. Their trysts become increasingly risque as the series (and their relationship) progresses, to where Keita has even brought Riko to orgasm by performing oral sex on her. Despite all this, they have yet to actually engage in intercourse, which remains in question as the manga is still ongoing.
The original OAV series of Tenchi Muyo! is filled with incestual attractions — the whole mess basically got started when Ayeka fell in love with and was engaged to marry her elder half-brother Katsuhito/Yosho. See Incest Is Relative for full details.
Seimei is a Love Makes You Crazy version in Loveless towards Ritsuka. To Seimei, him and Ritsuka are the only two people in the world. The fact that the two are full-blooded brothers is probably the least squicky thing about him, though.
Silvia in Genesis of Aquarion has a pretty obvious attraction to her older brother Sirius, becoming incredibly jealous of even the slightest hint of romantic interest in other women. It seems her insistent belief that he is the reincarnated lover of the woman she is the reincarnation of has a lot to do with this. In reality, reincarnation is largely to blame, but not in the way it first seems: they are actually both reincarnated from the same person, each holding a fragment of Celiane's soul. The longing of the two halves to be united again causes Silvia's apparent crush on her brother; he doesn't feel the same way because he got stuck with the negative aspects of Celiane's soul and memories, and so sealed them away at a young age.
In Lady Georgie!, the Plucky Girl Georgie is romantically pursued by her two adoptive brothers, Abel and Arthur. Since the three were raised together and Georgie herself didn't know she was adopted for many years... well, yeah.
This is a catalyst for one of the storylines in Mononoke.
In Urusei Yatsura, the Mizunokoji siblings have a one-sided version of this going on... more or less. According to their screwed up traditions, youngest daughter Asuka was raised in total isolation from the opposite sex, and with the terrible job her maids did in regards explaining the other sex (something worsened by her fact her first encounter with a guy was Ataru Moroboshi), she's terrified of men... except for "Big Brothers", whom her maids made out as a special, dependable, trustworthy exception to men in general. Between her phobia and her naive ignorance, she not only has a crush on her older brother Tobimaro, but is constantly trying to perform deeds with him that are only appropriate between lovers. Tobimaro, meanwhile, is perfectly aware of their relationship and that the things she tries are not appropriate, thus he freaks out when the poor girl comes on him. The fact that their crazy mother blames Asuka's actions on him, despite the fact she was the one who arranged for Asuka to be raised the way she was, only makes things more galling for him. The fact Asuka also has Super Strength and is thus prone to crushing his bones whenever she gets frightened or romantic does not help.
15-year-old Sakurako Saiki from Sakura Gari is a scary Yandere who is incredibly possessive of her older brother, the main character Souma, and has had sex with him more than once.. For further subversion, Sakurako is actually a male, Youya, who calls himself like that after the horribly fucked-up death of his mother... whose name was Sakurako.. And even more subverted: They're Not Blood Siblings. Souma is the son of the Saiki leader and his dead lost love, Abigail; Youya/Sakurako is the child of the original Sakurako and the retainer Katou. When Youya/Sakurako commits suicide, Katou reveals this and stabs Souma - apparently, to death.
Iina from Kokoro Library appears to have quite a thing for her sister Kokoro. She tries to steal kisses from her and gets quite upset when Kokoro decides to spend time in the bath with her other sister, Aruto, instead of her. Kokoro clearly loves Iina a lot too, but in a sisterly fashion.
In Freezing, Satellizer was abused by her half brother. He molested her as well, though their blood relation was in fact the only thing that kept him from out right raping her, what he did was enough to emotionally scar Satellizer to the point that she could no longer stand being touched by anybody.
And, for some irony, the one guy who's the exception, the one guy who can touch her because he treats her with dignity and compassion? He was attracted to her initially due to her resemblance to his big sister, and and given they share genetic implants tied to said sister that give Satellizer a genetic resemblance, they are an indirect example of this trope as well, except Kazuya Aoi (the guy) is a far, far better choice for Satellizer by far.
This is a plot point in Kagihime Monogatari Eikyuu Alice Rondo. The main characters are a boy named Aruto, his love interest Arisu, and his little sister with a very obvious crush on him, Kiraha. It is revealed later that Arisu isn't real, and Aruto made her up because he couldn't deal with his incestual feelings for Kiraha.
Shinogu and Hatsumi from Hot Gimmick are Not Blood Siblings. Shinogu is in love with Hatsumi but, in an effort to not burden her with his feelings, he tries to put distance between them. Hatsumi actually offers herself sexually to Shinogu at one point but he turns her down. And in the Hot Gimmick S novel, she actually leaves her abusive boyfriend Ryoki for Shinogu.
Namie towards Seiji. Izaya finds it a bit disgraceful.
Izaya's younger twin sisters Kururi and Mairu are also Twincestuously close to each other. In the anime it comes rather out of left field when they make their only proper appearance in the series in a DVD-only episode, and suddenly make out without any kind of foreshadowing, only for it to be never mentioned again.
The novel adaptation of Baccano! says that Graham Specter's first love was his sister. No information has been given beyond that so far.
In Gankutsuou Andrea actually tries to marry and rape his half-sister Eugenie. Though only to deliberately humiliate her and her family.
The brother-sister incest relationship is the central plot of the manga Tsumi ni Nureta Futari.
Ryo from Final Approach is quite obsessive over his little sister Akane and she's generally reciprocative. It's generally played for laughs as nothing more than an amusingly intense sister/brother complex, but it is worth noting that Akane insisted on taking part in the contest with the other girls to see who got to play the role of Ryo's bride.
When Akane is sick Ryo rushes home to take care of her. It's at this point the other girls realize they're not competing with each other but with Akane.
In the anime of Samurai Deeper Kyo , Big Bad Nobunaga Oda and his right-hand henchwench Shatora are an incestuous brother-sister pair who desire who turn the "boring world" of Sengoku-Era Japan into a literal "hell of battles" so they can openly be together in the chaotic new world. They reveal that their Start of Darkness was because society tried to force them apart by making their relationship taboo in the first place.
In Corsair, Jean-Hughes saves his seven year old brother Canale from being raped, but he can't stop imagining himself doing the exact same thing to him. This leads to him pinning the guilt and blame on Canale and loathing him even more.
Cain Hargreaves, the lead of the Count Cain manga and its sequel series Godchild, has this as part of his origin story. Turns out part of why he has the family curse so bad/ slash why his parents always acted so weird with him/why he has sort of golden eyes, is that his mother isn't his mother. His father's crazy sister Augusta is. When he finds out and goes to see her in her asylum, she jumps to her death in front of him.
For some reason, Kaori Yuki decided to reveal in the end that Magnificent Bastard Alexis was actually manipulated by his much more evil sister Augusta because... she was just that evil, apparently. Yeah, evil enough to seduce her brother into impregnating her and then spend the next twelve years catatonic in an asylum before killing herself just to traumatize the kid. According to her ghost, at least.
Junai Labyrinth is all about Umi, who has incestuous feelings for her older brother Haruto.
Flowers of Evil: the central theme is the sister's obsession with her brother.
Lola and Layla from Venus Versus Virus have implications of a Sister-Sister version of this. Lola seems to not recirpocate her obsessed twin sisters feelings though.
In One Thousand and One Nights, Dunya is infatuated with her older brother Sehara. She actually demands that he kiss at one point (which he does).
Mawaru-Penguindrum's first episode has Kanba Takakura kissing his younger sister Himari after she's resurrected and while she's sleeping. It hasn't been referred to later, though. Let's give it time.
It's given a rather philosophical twist in this series; Kanba's Internal Monologue in the scene revolves around defying fate and the animalistic survival strategy to determine one's free will. Basically, doing something that your very biology abhors is used as a sign for freedom of choice.
In the Penguindrum novel, the scene where a posssessed Himari pulls something out of Kanba's chest ( his life energy) is a little more suggestive than in the anime version. Not to mention, in the anime the kiss scene went into fade to black when Kanba's lips were milimeters away from Himari's. In the novel? It's described quite in detail.
Aaaand then... it's subverted! Himari and Kanba are Not Blood Siblings. Episode 19 explains that Himari was adopted into the Takakura family after she was rescued from a plance named the Child Broiler... and her savior was her and Kanba's brother, Shouma. Kanba himself is adopted too; he and Shouma relied on each other to survive, but he only felt truly as a Takakura when Himari welcomed him into the family.
Then finally reintroduced in the form of Twincest when Masako, Kanba's stalker and apparently jealous ex, turns out to be his biological twin sister, and Masako and Kanba were both well-aware of their relationship the entire time. Having physically assaulted and mind-wiped the rest of Kanba's ex girlfriends since she didn't see them as good enough for him, Masako ultimately turns her sights on Himari, whom she sees as both familial and romantic competition, but later sets it aside when Kaba pulls a Face-Heel Turn.
Oniisama e... has Rei Asaka's obsession with her older half-sister Fukiko Ichinomiya, and Fukiko's abusive behavior towards her as one of the driving forces of the plot.
Averted in Baka and Test: Summon the Beasts because while Akira Yoshii really wants to move her relationship with her younger brother to the next level, the normally super-horny Akihisa surprisingly expressly considers incest to be disturbingly immoral and constantly resists the nonstop attempts at seduction of his older sister.
To Love-Ru seems to heading this way, if Momo gets her way. Played for laughs when Mikan trying to resist the effects of Celine's pollen.
In Yuki Suegutsu's infamous Eden No Hana manga, the protegonist, Midori, was put in foster care and then was raped by her adoptive brother.
MM! main character Taro is actively pursued by his older sister AND mother. When he gets amnesia for an episode both try to pretend being his pregnant lover.
Happens quite frequently (both within the story's present time and in flashbacks) between Michel and Coco in the manga Copernicus Breathing.
Played for intense drama in Detective Conan. Kogoro's friend Raita Banba falls in love with a woman named Hatsune Kamon and they're about to marry. Suddenly, Hatsune dies when her car blows up the night before the wedding, and Raita is blamed for the incident as he had shown Crazy Jealous Guy traits. It turns out that Hatsune had just found out that her and Raita's massive similarities did NOT come out of nowhere, and they were actually twins who were raised separately after being orphaned as babies. Poor Hatsune, who was already very stressed out as she traced her and Raita's origins and dealed with being an Ill Girl, crossed the Despair Event Horizon when she got a call confirming that she and Raita were about to commit Twincest: immediately afterwards, she commited suicide.
Ouke no Monshou has the Ancient Egyptian princess Isis who is in love with her brother, Pharaoh Memphis. Her jealousy towards any woman remotely interested in him extends beyond the grave, and it actually kicks off the plot since Carol, The Heroine, fell victim to one of Isis's curses and then was thrown into the Egypt of the past...
For the first volume of Ichiroh!, Nanako's brother had it bad for her and even followed her while she was off studying for exams. Nanako, of course, did not return these feelings. Eventually, he realized his sister was maturing while he was not and set off to improve himself to be worthy of her. We never see him again except in passing and omake strips, presumably because incest jokes in a light-hearts 4-koma strip would be kinda out of place.
In Ooku: The Inner Chambers, it's revealed that Akimoto and his sister Kinu slept together, resulting in a daughter. When Kinu asked if he entered the Ooku because he was disgusted by what they did, his response was that if he hadn't, he'd be forced to marry, and he didn't want to father a child with anyone but her. Emonnosuke is quite amused when he finds this out about Akimoto, and points out that even Japan's origins center around this trope.
Deconstructed to the point of Fan Disservice in Sasami-san@Ganbaranai: In order to keep the power of Amaterasu in their bloodline, siblings in Sasami's family are forced to marry. Due in part to what is apparently a lobotomy, the sibling which does not possess Amaterasu's power is conditioned to care for and unconditionally love the one that does.
Near the end of Words Worth's first episode, Astral stumbles into Maria's cell. When he regains consciousness and sees her state of undressnote due to Stallion's attempt to rape her, mere moments prior, he decides he likes what he sees and rapes her. Though it isn't explored in the OVA adaptation, the source material heavily implies that Maria and Astral are the biological offspring of Pollux and his wife Maria - the same woman who bequeathed her ring to her daughter of the same name. Meaning, Astral raped his biological sister without realizing it.
Following the timeskip (20 years), Maria now has an 18 year old daughter named Miyu. All evidence points toward her being the result of Astral having raped her. Not only is Miyu around the appropriate age, but Maria is still said to be unwed by that time and implied to have not been with anyone else, since the incident. Astralnote who's amnesiac by this time, due to taking the full brunt of Maria's MystralWindow, which propelled him 20 years into the future and left him without his memory meets Miyu after saving her from a rampaging bear, while she was bathing out in the forest, and ends up sleeping with her. That's right: he banged his own niece, who's also his daughter... without being aware of it. Again. Talk about keepin' it in the family.
In the Manga for Elfen Lied, this is the entire reason Lucy/Nyuu/Kaede's half-brother was born.