I know it's hard to diagnose bottom bracket noise (or any bike noise) through the internet, buuuuuuut this is killing me! It's a carbon bike - Trek Madone 4.5, Shimano 105 cranks/bottom bracket. I'm building it up at work. The head mechanic was gone today, the other two guys I work with couldn't figure it out either.
The sound is directly proportional to the rotation of the crank. It's not a clicking or pinging or anything. More of a vibration/rubbing (not chain rub, deeper), and it most noticeable by feel than by sound - feels kind of like a hub that's too tight, almost like it's seizing. It's 'bumpy' when riding and turning the cranks, and you can feel it through the downtube when it's in the stand. It only happens three times per full crank rotation, in the same three spots. The bottom bracket cups/bearings are tight, nothing is loose. As far as I know, nothing is stripped. The rear derailleur cable tension and limit screws are set correctly, and it shifts perfectly in both the back and front. The cassette is tight.