So basically, my PS3 stopped reading dual layer Blu-Ray discs.  So after talking with several different customer service reps (who didn't seem to understand what I meant by dual layer blu-rays, though they tried everything to be helpful) I decided to just send in the console and have them repair it.  It came back about a week and a half before Christmas and no works just fine, I was able to finish Uncharted 3 (which was rather heartbreaking to come back from the store with Uncharted 3 after so long only to find my PS3 wouldn't read it) and when I ejected the disc the drive made a rather loud clunking noise.  It still works fine but it makes this same noise each time I eject a game.  Anyone know if this is normal or should I be contacting Sony again to find out if something is wrong before my 3 month warranty is up?

That sounds questionable. I just got a PlayStation 3 and my disc drive doesn't make any noise, and usually a noise like that concerns something that's about to break, or severely out of whack.

It depends on the reality of the noise. For me, I've always had a clunk noise when my PS3 ejected discs (and I've heard the same sound from many other PS3s as well). So it is possible that they replaced your unit's drive with an older one or a particular model that didn't sit perfectly flush... or whatever the case is. In any regard, if it is as bad as you make it sound, YES, contact Sony again.

A clicking like that means that the disc is stuck or it has trouble ejecting the disc. It happened to me when I bought a version of Jak & Daxter that had one of those mom & pop video store stickers on it. The sticker I guess somewhat peeled off and the disc got stuck in the PS3. I say call Sony back and let them know the situation. Most likely they'll take it back and repair the mistake.

I'd wait maybe a month or two and if the sound continues or gets worse, I would suggest sending it in before it causes any major malfunctions in the system.