Those of you who use em when sizing fonts will know that they can be a headache when dealing with nested elements, and having to make the px -> em
I never use pixel sizes for fonts in any program (except Photoshop I suppose, since it just had it in pixels by default). I've always used point size (such as in Word) and have since moved to scaling relatively in CSS with em. I set the body font-size then scale using em.
Maybe I'm just used to knowing how big point sizes are on screen and in print. I can never guess the size of a pixel font height so I don't use it.