I don't Rape my PCs, I don't think it would elicit the emotional response I'm looking for. Of course I never did tell them that, when I had a group they were convinced that I had a 20 page handwritten rape scene ready to go in case they managed to get themselves into that kind of situation. (The hand written part is what pushed it from creepy to disturbing)
I have on occasion had NPCs rape other NPCs, I use it sparingly as I want to convey as sense of personal horror and violation, it should represent a fate worse than death. I also never describe a rape in detail, I feel that detail allows people to stop looking at a rape as an act of horrific violence and simply view it as a sexual act. Once again removing the emotional response.
Besides the after effects are far harder for players to deal with than just listening to a rape scene, you can have an NPC display; Fear of being alone, Fear of being with someone, Self mutilation, Suicide, Hyper-sexuality, no Sexuality, depression, violent personality changes, and fear of well anything. An interesting situation is an NPC rogue + violent flashback + nervous breakdown + sneak attack = Fun in the dungeon.
As for PCs raping NPCs, I won't simply say no, I will however try to get the other PCs to reign that player in. They usually have the tacit approval of the group for committing that action, I explain to the group that the character is committing rape for some of the same reasons that people do in reality, they have the power to do so and they have no fear of the consequences. I try and impress upon them that if this PC can rape an NPC over which they have power why can't that PC rape a PC over which they have power, most groups unwilling to let it go if it puts their asses in the danger zone.