With me it was my SPD cleats after 2500 miles. i replaced them, no more click...

Click came on after 5 months and 2500 miles and only under load. I had the bike shop service the bottom bracket, replace the chain, grease and re-tighten everything especially the headset, all the cables and the front wheel. After all that, click kept coming back. It would start after a few miles of riding and was worse when I would go to the drops. I was almost ready to sell the bike when I read here about cleat clikcing. I tightened the hell out of them but still click, click, click. I re-tightened, greased and re-adjusted the SPD pedals...no change. Tightened the bottle cages and seat...no dif. Made me nuts.

I called Shimano and the phone rep recommended cleat replacement. Did that and after 3 rides, no more clicking...