I also have a el chēapo silicon case/skin for my phone where it allows 1-2mm of clearance between the screen and said surface. I rarely put it glass down so I voted glass up. But there are occaisional times where I'll put my precious 'child' (Like that even needs the quotes!!!) glass down. I can't think of any at the moment but I'll admit I do...
I always place my iPhone glass down. I've had my iPhones, first my 3G and now my 3G S, in a case with a screen protector from the moment I got them. I had them on before I left the store. The case I use is a DLO silicone case. It has the thicker corners and the raised lip on the front so the actual screen never touches anything. I only place it face up if I am waiting on a MSG at work so that I can see it light up on my desk and be able to read it without having to mess with it. I feel like it is safer because the phone is fully protected with a case and all of that and with the lip on it I can have it glass down so nothing can get to the screen.
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...
Glass up with lipped case and screen protector. Never though of some object hurting it, just never really felt the need to aim glass down. One difference is when riding my bike, in my pocket its glass down, incase i crash, the glass is protected by my body and the case protects the back.
i have always kept it glass up unless its on something soft like a bed or sofa. i have the griffin clarifi case with a screen protector, so there is a little lip if i wanted to, i just prefer it face up
Glass down, but only because my 3GS is in a hard shell case by Incase. The case provides a small lip around the glass, so even when face down, the glass never comes in contact with the surface it's resting on (assuming it's flat!).
Glass down when at home because my dog is a drooling machine, and at bars or restaurants because of food and beverage's ability to splatter. Otherwise, glass up. I do use a lipped hard case at all times.