After taking them for a test drive to point out the sound I was noticing, the tech heard it as well and i dropped the car off. When I went to pick it up, they told me that the #3 motor mount wasn't as tight as it was supposed to be, and that physically pushing the engine made a very similar sound alone. So they loosened and readjusted the #3 motor mount as well as the rear transmission mount.
Golden question...did it fix it? Well, it did quiet it down a little bit, but it's still not completely gone. That said, i'm gonna have to rule this out as a regular noise of the engine/tranny as it sits. Apparently i'm just a little too in-tune with my car. Now that I know it's not something that even the dealership is alarmed about, it's time to finally move on.
For anyone else wondering if they should take their car in for the same thing...i'd say go for it just to have any adjustments made. It's under warranty, so why not take advantage of it?
Update - 12/4/10
After about a week, i've noticed that the "adjustment" they did has actually made is easier to now hear the thunk/popping sound in 5th and even 6th gear now. I didn't originally have problems with those 2 gears before. I'm thinking that they loosened the motor mounts and adjusted them, then left them looser...thus creating even more of a problem.
I'm all but ready to get under it and start dinking around with it myself now. This is getting insane. So if their adjustments have made it louder and more obvious in 5th and 6th, then obviously something has to do with the motor mounts. Now, if I can just locate all of the motor mounts to tighten them on down.