I know this thread is old, but I thought I'd post here instead of making a new thread.
About a month ago I started having this problem on my 12" rMB. I've had the machine for about 5 months and it would creak rather loudly as you opened it up, and once opened if you moved the lid up and down it would creak as well. I did feel it was getting worse as time went by.
I had a similar issue back with my 2010 11" MBA and the Apple Store was able to tighten the bottom plate for me, which to my recollection solved the issue. I wasn't really concerned about it but thought I would bring it in anyway to get it checked.
Expecting to get the plate realigned, I brought it in to the Omotesando Apple Store in Tokyo. I was 1.5 hours late for my appointment due to work, but they took my case and I happened to get the store manager. He was really great, one of the best geniuses I've ever dealt with. He said there was a problem with the hinge, apologized for it, and offered to give me a replacement instead of sending mine off for service.
The next day I brought in my box and accessories and within 5 minutes I left with a brand new 12" rMB, even with a brand new one year warranty.
No creaking in the new one so far and I just wanted to say I'm very pleased with the manager of the Apple Store in Omotesando. He was very kind, understanding, and just awesome and made me remember why I love buying Apple products. I know not all geniuses at the stores are as nice or accommodating, but if you get one like this it really makes any extra "Apple tax" worth it for me. I've had repair experiences with other manufacturers such as Dell, HP, and Lenovo, and none of them have been as good as this.
Anyway, I'm not sure how many people still have this issue, but here's to no more creaking hinges!