Saying "good question" during a seminar talk
As an economist I can rant for hours about people's ulterior motives... as a speaker I can tell you that this reaction springs in me spontaneously, when the question has good timing with what I am presenting, meaning that it is a good opening for the next issue (or next aspect of the current issue) I was about to start speaking on. It makes a presentation rolling with the audience, and you cannot ask much more than that.