Though it was Bowdlerized to remove as many references to incest as possible, the idea was too central to the plot of Drakengard to throw it out completely. The game has only one or two allusions to it.
In the bishoujo game Ko-ko-ro..., the protagonist, Souji, has had sex with both of his sisters and, during the game's timeline, is still having sex with his younger sister, Asuka.
Resident Evil: Code: Veronica? The relationship between siblings Alfred and Alexia Ashford is by far the creepiest part of the entire game. Many more layers are added to the Cake of Creepiness when you add the fact that the twins were born when their "father" was trying to clone his super-genius ancestor Veronica, who his family all but worshipped, and... the embryo divided, which has implications that one or both of the siblings is transgender or intersex.
In Jagged Alliance 2, you can run into a family of heavily inbred rednecks. One of them will tell you that the inbreeding is what keeps them strong. For some reason they have run out of women though and want you to give them one of your party in exchange for guns.
Janus and Lela in Divine Divinity. And they have sex when they are like only (pre-)teens (Don't worry, it's told to you, not seeing it).
Though as an ero-game it's par for the course, Princess Waltz takes this to an almost absurd degree. Arata and Chris are not only half-siblings (same father), they are cousins (their mothers are sisters), and second cousins (their father and respective mothers are also cousins).
In Metal Gear Solid 2: Sons of Liberty, Emma Emmerich, step-sister of Hal Emmerich... well let me quote wikipedia: "It's revealed through conversations between her and Raiden and later between her and her brother before she dies that she has strong romantic feelings towards Hal and wished for him to see her as a woman and not his sister."
Which, of course, never happened, because Otacon was sensiblesleeping with his stepmother/E.E.'s mother.
The Visual NovelLamune has a romantic path for Suzuka, the one-year-younger sister of male lead Kenji. The anime adaptation portrays their relationship as a non-romantic sibling relationship, since it follows Nanami's route, though the trope gets poked fun at once when Hikari teases Suzuka about being jealous of Nanami.
In Viva Pińata, (despite how it looks) this can happen veeery easily. Heck, getting the Fourheads practically requires it! (Unless you want to put in way more effort than necessary, of course.)
No wonder it's a mutant... product of repeated incest, and you have to bash its egg open early.
Parodied on VG Cats when Leo kills a pińata's parents and feeds them to it. Aeris is shocked he did this and Leo emphasises that they were "his inbred parents".
In the Fallout 3 add-on Point Lookout, the Swampfolk are a race of redneck mutants that used to be humans, but through inbreeding they mutated into violent and primitive humanoids.
The small hamlet of Andale in the Capital Wasteland seems harmless enough, with two cheery families. Then you talk to young Junior Smith who tells you that he doesn't want to marry the little girl, Jenny Wilson, across the street. More than it just being a case of cootie-fears, he reveals that part of the reason it's weird is because his father is the brother to Jenny's father which makes him "... something, I'm not sure what." If for some horrifying reason you're not bothered by the fact that Andale's residents have been, for the last few incestuous generations, killing wastelanders foolish enough to travel within their territory and then eating them, then you can learn from Martha Wilson that the old coot living next to them is father to both her and Linda Smith (Junior's mother). That makes them double first cousins which is as bad as being half brother and sister, but not as bad as 3/4 brother and sister (aka, sibling cousins).
In The Sims 2 half of the neighborhood of Strangetown is made up of the Curious Family. But since EAxis didn't bother to set all the relationships correctly, many players have unwittingly married the Curious brothers to their older half-sisters, Lola and Chloe (Curious) Singles. It's also possible for the sisters to have romantic interactions (without cheats) with their surviving father (PT #9 Smith), and probably everyone they're related to that's old enough. Thanks, EAxis.
Very strongly suggested to have happened in Wild ARMs 2 between Lord Irving and his sister, to defeat the Big Bad (long story).
Played with and ultimately averted in Cute Knight, where the PC can either marry Prince Kirelan or take her royal position as his sister, Princess Alexandra. But it turns out she's not really Alexandra, she's just faking. But then it turns out that she IS a princess by blood after all, she's Alexandra's older sister. But THEN you realise that it's okay, because Kirelan's adopted!
Before the console release of BlazBlue, many fans shipped Jin/Noel, Ragna/Noel and Ragna/Jin. At the very beginning of Ragna's story mode, it is revealed that he and Jin are brothers and Noel is a cyborg clone of their sister.
However, it is arguably canon that Jin has the hots for Ragna anyway.
Jossed as of Continuum Shift. Jin was just driven batshit crazy by Terumi Yuuki and Yukianesa. Tsubaki is the one he somewhat cares for. Not that this revelation will stop the fangirls... OR the game developers, for that matter. They are having way too much fun playing on Jin's Yandere-ish tendencies.
While pouting in a park, Noel wonders why she gets so damn flustered and says stupid things to Ragna. The thought briefly crosses her mind that she's acting like a girl with a crush, but she immediately begins denying it to herself.
This immediately takes on considerably darker tones when one takes Nu-13 into the consideration. As her name implies, she is the 13th clone of Ragna and Jin's little sister, and she is veryYandere for Ragna. It is revealed that due to the clones' programming, they compulsively try to get as close to Ragna as possible, with the final objective being to merge with him in order to complete the Artifact of Doom that the clones and Ragna respectively carry each half of. Then again, it is strongly implied in Continuum Shift's true ending that pure emotions can override the programming.
Though the details aren't expanded upon, so we don't know for sure if BSI occurs, it's still explicitly stated in Tsubaki Yayoi's story path that when children within the noble Yayoi family began exhibiting weaker Ars Magus aptitude, and a shortage of strong Ars Magus users outside of their family prevented them from rectifying that problem by marrying into greater magical power, the clan members started resorting to incest and inbreeding in the mad hope that they could preserve their family's strength. Tsubaki, it turns out, is not the first daughter of her parents; she's the first one to survive.
Suika: Technically, they aren't blood related, but Yoshikazu feels this way about Akane causing him some major angst. The reason is that he feels she is genuinely his little sister, which disturbs him greatly.
Tsukihime/Melty Blood's Tohno Akiha is strongly implied to have the hots for her brother Shiki, although the reverse doesn't seem to be true... except in Akiha's route where they DO get it on. Possibly averted, as well: Even though they're Not Blood Siblings, and both of them are aware of this (Akiha all along, Shiki much later), they continue to treat each other as such.
Shiki comes to love whichever heroine's route he is in and does not love whichever heroine's route he is NOT in. That being said, saying that he does not return her feelings is as untrue as it is for any other heroine, since all of them have feelings for him regardless of which route he is in. Akiha also doesn't push on it until Shiki starts pushing back.
Elis and Hiroki in Canvas 2, though of course she's actually his cousin.
This is heavily implied with Cesare and Lucrezia Borgia in Assassin's Creed: Brotherhood . Cesare kisses his sister Lucrezia in a lover's fashion before a military expedition in Romagna, is receptive to his sister's... suggestions, and it's implied that the whole chain of Memories where Ezio must save Pietro, Lucrezia's admirer, from Cesare's personal assassin Micheletto Corella are all because of Cesare's jealousy, albeit deliberately provoked by Lucrezia who mistakenly believes that he's cheating on her with the captured Caterina Sforza.
If all this wasn't enough, one of the accusations given to Cesare when he's imprisoned by the men of Julius II is of incest.
There are no specific examples, but this was mentioned in Bully by the preppy girl when she talked about marrying her cousin. A baffled Jimmy asked about that and she replied that it used to be between brothers and sisters before it was outlawed.
All over the place in Kara no Shoujo. The one place you don't find it is with Reiji's little sister Yukari. If you want a sex scene with her, you're going to have to settle for an early picture of her in the middle of getting changed.
There is a skit in Tales of the Abyss in which Natalia and Anise question Tear about her 'type' of guy. Although unknown to the latter two about their real relationship, they seem to think it quite obvious that Tear was attracted to Van, which caused said melodist to freak out and run away from the conversation. It really didn't help that he was also her surrogate father.
The "terrible family secret" on the checklist in Long Live the Queen refers to Kevan, the Earl of Io sleeping with his full-sister Corisande, the Duchess of Mead. And this is only the last step in a long sequence of just how screwed up that family is.
Occurs during a bad ending in Swan Song, although you won't know this unless you get the Good ending.
In Duel Savior Destiny Mia is one of the available options and the only girl Taiga will not pursue, though it later turns out that this isn't because he's not attracted to her. She's simply genuinely off limits to him as a sister until she basically rapes him into deciding that it's pointless.
If you click the right window, you'll come across an example of this between Reed Hawke and his sister in Voyeur.
The visual novels by Overlow have this all over the place. Tomaru Sawagoe may have one of the most tangled family trees in all of fiction, having had children with his half-sisters, his aunts, his daughters. And his sons have followed his example by doing it with their half-sisters, and those sons includes, possibly Makoto from the School Days games.
In Grisaia No Kajitsu we find out that Yuuji's older sister Kazuki more or less molested him before she died, though he didn't mind since he nearly worshipped her. In Grisaia No Rakuenit seems she really does love him, to which he responds neutrally at best. They do have sex at least once, though, since Kazuki wants it and isn't as dead as previously claimed.
Played For Comedy and Averted in one of the skits in Tales of Destiny 2. Some time after Judas's true identity is revealed, Loni asks him if he competed with Stahn for Rutee's affections. Judas immediately reacts with horror and disgust, but since it is not common knowledge that Leon and Rutee are related, the party is somewhat confused.
A visual novel known as Mother Daughter has the protagonist's mother and sister depend on him after his father dies... so he has sex with them. His sister andhis mother. And the girl next door. And her mother.