Not that I'm any good at it, but I would always down pick when playing palm muted power chords. If I'm trying to play really fast power chords without palm muting (more punk style than metal style) I try and alternate pick for the sake of speed (and my wrist). That said, up until a few years ago I down picked everything because that's just how I'd taught myself. I still find myself reminding my hand as I play to try and alternate/up pick notes.

Related thought, anyone know how Metallica manage the "galloping" style chug in "The Four Horsemen"? That's got to be alternate picked power chords doesn't it?