If I have a choice - percent. Ems are unwieldy, percent is straightforward, and I prefer to allow the user set what they want and design so if flows with it. I generally start from a base of 90-95% for most body text.
Too often I deal with designs in which the designer couldn't care less about the end user, only their precious design which has obvious roots in print media and Graphic Design 101 with beautifully bottomed out columns in spite of the fluid nature of dynamic content, textual elements intended to line up with fixed graphic elements all over the place, and of course it must maintain stability in all browsers, so I'm forced to use px. This is, sadly, a majority.