I had a MacBook Air that had horrible creaks. The first time I brought it in to the Apple store a genius reseated the bottom. Later that night, the creaking was back. The second time I brought the MBA in, the genius replaced the bottom panel of the computer because he said a snap located in the middle of the bottom was broken. That didn't get rid of the creaking either.
The next two times that I went in, Apple replaced the entire body casing, but the creaking never went away. After Apple wanted to send out the MBA a third time, I told them it was stupid to keep doing this. It was a waste of my time and theirs. The creaking seemed to be inherent to the design of the MBA. A genius agreed and told me his wife had the same issue and she adressed the problem by keeping the computer in a Speck shell. I didn't want to live with the creaking or have to put the MBA in a shell, so I asked a manager to take the computer back and give me a store credit (this was a few months after my purchase).
In my case, and I'm guessing for most others, MBA/rRBMP creaking is most noticeable (or only noticeable) when you're using the computer on your lap. When I was at the Apple store, they told me to use the computer on a flat surface, as the computers aren't laptops. They're notebooks.
Anyway, like one of the posters above mentioned, a genius suggested that maybe the creaking gets worse after the computer is used for a while and warms up. Whenever I would take my old MBA into the genius bar, I had to tell them that I couldn't usually reproduce the creaking on the spot. That said, it would happen about once a minute while using my computer at night in bed (typically from palm movement below the keyboard). The theory is that the aluminum body shrinks a little bit when the computer is warm from use, and that leads to a little bit of play in the case which can cause the creaking.
All that said, I've had an rMBP for the last few weeks and I haven't had any issues with creaking. Hopefully creaking isn't a widespread issue due to the thinness of the rMBP, and the creaking the OP is experiencing can be resolved by a reseating of the bottom panel.