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.
The new character in Tekken 6, Miguel Caballero Rojo, adheres this trope in an one-sided way. When his sister announced she's going to get married, he became so furious he almost planned to kill her fiancée. Unfortunately, during the wedding, there's a sudden attack, and that killed his sister. Roaring Rampage Of Revenge occurs soon after for Miguel.
In No More Heroes it is implied that Travis and his half-sister Jeane might have been in that sort of relationship. Travis was completely unaware of the situation he was in, and is appropriately shocked and horrified upon finding out.
In Max Payne, one of the Mooks is watching a soap opera where a woman reveals to her lover that she is... his long lost sister!
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 transgendered 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).
The player character and Imoen of Baldur's Gate grew up treating each other like brother and sister, but are hinted to have/have had romantic overtones in their relationship (yes, even if the player is female), which is overturned in the sequel, when not only does the player have a chance to fall in love with someone else, but Imoen is in fact revealed to be the player's half-sister (though given the nature of their father, it's debatable if they're related at all...).
Played straight, however, by the Imoen Romance mod. To the mod's credit, it does not take an easy way out of the Squick involved, and presents it as something the player and Imoen simply have to deal with.
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).
And with what the plot of Mega Man 10 is...It's only going to get odder.
Actually, the Legends games take place a while after the classic games, and the Battle Network games take place in an alternate timeline where Dr. Light helped make the internet, as opposed to being a roboticist.
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 sensible sleeping 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. (This troper does not know if the visual novel ever makes a Not Blood Siblings reveal.) 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 Pinata, (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.
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 now that this troper thinks about it, probably everyone they're related to that's old enough. Thanks, EAxis.
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 Blaz Blue, many fans shipped Jin/Noel, Ragna/Noel and Ragna/Jin. In true story mode, it is revealed that they are all siblings (although with Noel's background, it might be a little more complicated).
However, it is arguably canon that Jin has the hots for Ragna anyway.
Can happen between the hero, Ryo, and his stepsister Ayame in the visual novel Crescendo.
The hentai game Artificial Girl 3 has the option of giving a girl the player creates the "Blood Related" trait, which depending on other factors makes the girl have some big or little sister lines during normal and special interactions.
Kikokugai The Cyber Slayer, just mentioning its name in this article is a huge spoiler by itself. The game takes this subject so seriously that you won't begin to think of how much impact it has on the plot.
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