Hmm. I'm surprised no one mentioned the rape scene in volume 1 of Tenjho Tenge. There was a lot of hoohah about that as the translated version covered up the victim a lot more, to allow the manga to sold without a too mature audience label.
But that is not a bad example of portraying the horror, violence and humiliation of the act. It is uncomfortable to read, and it should be. But the strength of the victim in later volumes really comes through.
(of course, that wasn't just attempted... the rapist succeeded.)
My feeling in general is that it can and should be included in certain series, as long as there is sufficient reason for it (to explain a catharsis of character, a behavioural difference, a true villain's actions, a reason for revenge perhaps). But whatever the reason, it should be depicted as the despicable thing that it is.