I voted glass down but here's my thing:
I have iSkin soloFX cases I use. They are a silicon that covers the bezel, and there's a spacing when you set the phone down to where the glass is actually not even near touching the table, the case is.
If it's out of the case, then I definitely put it face up, as I don't want the glass directly touching a rough surface.
Case = face down
Naked = face up
Glass down, but only because the Speck CandyShell case I use creates a lip for that purpose -- if I didn't have a case that created a lip, I'd be glass up...