All these guys voting for comfort... sorry, lost me there!!! lol seriously - wear whatever makes you feel best, which for most girls I know does not necessarily mean what's most comfortable. Personally I think heels look great on girls, it's not about adding height, it just transforms the way a girl carries herself and gives a slimmer, more elegant and sexy form. So my vote goes to heels, and a variety of heels can all look great - only exception is wedges which can sometimes be cute but too often look big, clumpy and kinda ugly.
I've never 'told' a girlfriend to wear heels over flats, it's not my place to do so - what a girl wears is entirely her own choice. But you asked for guy's own preferences so there you have it - if all else was equal, heels every time! :)