In reply to Colin Henderson:
Might be miles off but I had something similar which I thought was coming from a pedal (mostly because it happened almost every time I put downward force on the pedals and turned the crank) but it turned out to be something where the handlebars connect to the frame (sorry, uber technical terms here...). Mate said it was a bearing that had gone.
It was just hard to actually pinpoint the source of the sound, oddly enough. It was only when my pal was cycling along side me and I said something like "as you can tell, my pedal is ***ed" and he told me the noise was coming from the handlebars.
It just so happened that me turning the pedals was also putting strain on the handlebars, causing the click....which had led me to believe it was the pedals that were clicking, (and a bit of weird tinnitus that made sourcing the direction of the sound a bit iffy)
Hope I've explained that clearly enough...it's easier in person and with hand gestures.