I wouldn't ever really say "did you wait long?" because it doesn't sound particularly natural. You can use the following examples fairly interchangeably: How long have you been waiting (for me)? I hope that you haven't been waiting (too) long! I hope that I haven't kept you waiting (too long) I'm sorry to have kept you waiting You haven't been waiting too long, have you?

I agree with Jay's suggestions. Please don't think that we avoid using grammar such as "have you been waiting" in daily speech. Really, we use it all! :)