I go for em. The base font size in em is 16px = 1 em, so it’s quite simple to calculate for example 12px (12/16).
I keep my %-units to items and contents widths.
I’m not saying my way is the correct way, but it has worked for me so far :)
I recently heard from a jQuery UI team member that “If you have px in your responsive stylesheet, you’re doing it wrong”.
I do not agree with this as heights can still be valid to determine in px. Another discussion maybe but thought I’d throw it in here.