One of my professors made a rape joke. What should I do?
Speak with the professor, and give them the benefit of the doubt. Ask for an appointment, and bring another student if you feel uncomfortable doing it one-on-one. Most professors (hopefully) would not intentionally make such jokes -- give them the benefit of the doubt, allow them to explain themselves or apologize, and go from there. Following Hanlon's razor, my guess is that they were trying to make an inoffensive (or at least less-offensive) comment and botched it. 

If this doesn't go well, you can escalate. The department chair, a trusted professor, or your university's Title IX office (in the US) are good starting places. In general, they will be looking for a pattern of behavior.

Edit: I'm surprised how much controversy this has generated. College students are adults, and the professor's (possible) transgression was an off-color joke in public -- not fondling or propositioning. I agree there is no place for such jokes in the classroom, so - what is the desired outcome here? Presumably, that he will explain or apologize, and not do it again. This was months ago, and he (apparently) hasn't done it again, so maybe no action is needed. If OP wants to make sure, and to get the explanation/apology, that's admirable - ask for it adult-to-adult. If they don't give it, escalate. But for something like this, it is my view that running to the ombudsman, without first raising your concerns directly with the professor, would be downright cowardly.