I was actually going to add "It's no Drakengard, though" to that post, but decided against it. I don't remember why. Drakengard also has incestuous love. Granted, it's one-sided and never consummated, but still... That game was just all sorts of wrong, when the most normal character you'll ever find (other than nameless mooks) is a human-hating dragon.
That rape scene in Shadow Hearts 2 is played for laughs, really, so it's not quite as dark. Hell, Joachim was told it would happen, yet he went ahead with it, so it falls more on dub-con. The part that disturbs me most is that it all happens in front of Anastasia, who is, what, thirteen? That's a pretty young age to be corrupted into a yaoi fangirl. But why the hell did she just stand there squeeing and not take pictures?
The rape in Soul Nomad is heavily implied, but I don't remember it actually being spelled out. Hawthorne buys little girls, raises them to adulthood, then rapes them on their birthday. Cue next girl. Conversations with the NPC "Covered Woman" as well as some of the other NPCs who decided to take care of her suggest that she was a victim of this. In the Demon Path, Trish doesn't manage to escape this fate and loses her mind.