Yo, Batoto.
Do you know any Shoujo Manga with rape in it?
It could happen passingly, it doesn't have to be the biggest focal point, it just has to happen at some point (it happens a lot to make some drama, I'm sure).
The more popular/main-stream, the better, but one-shots here and there are fine too.
Post 1990's would be good. If it's been serialized by Cheese!, even better.
I've got Akuma na Motokare, Bitter Virgin (not a shoujo, I know), Desire Climax, and lots of Shinjo Mayu.
-- I'm writing a paper on this.