PCs should not get raped unless the player is okay with it OOC (e.g., you have planned it together), or the player has been told at the beginning of the game that rape is a possible consequence of their success/failure in-game, and they have willingly accepted that risk. In any other circumstances, thou shalt not rape PCs. This goes double for pregnancy resulting from rape.
KNOW WHETHER OR NOT ANY OF YOUR PLAYERS HAS BEEN SEXUALLY ASSAULTED. One of our players once made a character who had been raped in her past, and when she tried to engage in solo combat with the perpetrator (and lost horribly), the GM quite reasonably played the villain to type and indicated that it happened again. We didn't find out about the player's past until later.
As for NPCs... the big thing about rape is not to overuse it. Personally I hate it as a plot device, despite that fact that I used to use it liberally, because it's so damned overdone now that most writers/GMs use it as this big shortcut button to "DRAMA!" So use it sparingly, unless you want it to lose all its impact (see also "Rape is the New Dead Parents"). Avoid inflicting it upon irritating or unpopular characters as a way of making them "more sympathetic".
If you must use rape, don't let it be a threat only to females, or only to attractive characters. Rape is about power, not attraction. If you would not use rape in any given situation for a male character, do not use it for a female character either. Similarly, do not imagine that women cannot or will not commit rape.
Do not let rape make your NPCs into idiots. Do not have the coldly-brilliant villainous mastermind stall his genius plan because he just can't stand not getting some before he takes over the world.
Don't be surprised if one or more of your players - especially female players, I'm sad to say - gets off on it. Especially if they have self-esteem issues, as so many gamers do.
Whatever you do, do not treat rape as the go-to motivation for every female character.This is the worst fucking trope that gamers, fantasy authors and comic book writers ever had the collossally poor judgement to perpetuate. Women do not need to be motivated to take up an adventuring life any moreso than men; they do not need to be damaged or ruined in order to become strong, to desire strength, or to take risks. Strong female characters do not need to be "re-feminized" by suffering sexual abuse.
Those are my pointers for now, hopefully useful. I'll add more if I think of anything else.