I'm on the same boat as the op. I'm on my 3rd iPhone. The first replacement I got at the apple store. The guy pulled out of a black plastic box. That one was overheating and draining battery pretty fast, so I called apple instead of going to the apple store. They gave me 2 options: go to the apple store or mail in my unit for repair. I knew there was a third option, but I had to get it out of the rep since she seemed reluctant to mention it. Anyways the third option was to put a hold of $599 on my cc, plus pay $29, and they would ship a replacement phone to me.
I was expecting my iPhone to arrive in a retail box, but it didn't. Apple sends you a "kit". In the box I found a white empty box, a black box that contained the iPhone, some strips o tape, and foam padding. My first thought was that they send me a refurb. But after further inspection, I believe they sent me a new one. Here's why: the black box the phone came in had two black stickers sealing it; the iPhone came in a little plastic bag, which is common with stuff from Asia; but the biggest give away was that the outside of the box still had a customs sticker on. A big green sticker that said "product of China (mainland)". On top of that sticker it had another sticker with the phones serial number on it.
The serial number for my original iPhone stared with a C3, for the second one it was C7, and for the third it was C3 again. I believe apple has these kits put together in china with brand new iPhones, and then shipped over here. So if you have a problem with your iPhone and want a good chance of getting a new one call apple and ask about express replacement service.
Also IMO if your phone has a fault within 90 days of purchase, I think apple should guarantee replacement with a new unit. That seems fair to me. How is it fair that if you get a dud out of the box, apple washes it's hands and gives it's customers a refurb unit worth 2/3 as much.