In my opinion, under NO circumstances should you ever take out a notepad and write down anything. It's completely inapropriate and distracting to the interviewer. What is he/she going to be doing while you're writing down information? Wait?
Never do anything out of the ordinary at an interview where you're not sure what the preception would be. I agree, have a list of prepared questions when you come in to the interview, but have them in your head. Make a mental note of interesting topics during the interview and ask about them afterwords, but don't write them down.
Pulling a list of questions out is probably going to make the interviewer wonder about how your memory works under pressure, and unless you have superstats (which means you were unofficially accepted before you walked in), it's most likely the kiss of death.
Again, this is all my opinion.