Originally Posted by FBinNY

Clicking, synchronous with the crank is one of the hardest things to diagnose on a bike. It can come from anywhere. Knowing the details of the components and type of BB helps because some are more prone to clicking than others.

However, before doing ANYTHING else, I always remove both pedals, clean the threads and faces of both the cranks and pedals, apply fresh grease and reassemble TIGHT. The pedal/crank interface probably accounts for about 1/3 of the instances, but even if the odds are lower it's still place to start because it's the easiest to eliminate.

If that doesn't work, borrow a pair of plain pedals known to be OK to rule out your pedals.

After checking the above, then you can look at the BB, but other than pedals the devil is in the details. Some cranks may click on the spindle, some spindles in the bearings, and some entire BB systems move within the frame. Besides the pedal/BB area, clicking can also come from anywhere on the bike, because when you pedal hard, you're flexing everything.

BTW - one simple and overlooked cause is the chain on the rings as it passes pickup pins or shift gates. Chain on ring clicks are usually more pronounced when the chain is coming from either side of the cassette than the middle.