Gentle noises show you're still listening, if you use them at the right time.

The key being "at the right time." I used to know a guy who had the strangely off-putting habit of doing this with the completely wrong rhythm, giving the impression that he wasn't actually listening – and I don't know, maybe he never really was. It was as if he was counting down a random number of seconds to mutter "mm-hm" in a vacuum.