I always get that clicking noise on my carbon fiber Trek. I use the old original SPD road pedals (no longer made, too bad...). In cold weather (under 5 degrees Celsius, 40 degrees F for you Yanks) the bike is completely quiet. Warmer than that, and the bike starts clicking. I figure it's just dust in the pedal bearings, and the carbon fiber frame amplifies it. Aluminum frames do the same thing. Steel is quietest. I tried replacing the bottom bracket and it still clicked. Now I just live with it.

- L.