This last week I had three morning shifts. I've been noticing this little clicking noise for many months now. I thought it was my crank arm just tapping the derailleur as it came around (my bottom bracket spindle could really stand to be a few mm wider). However I recently observed that this is not the case. The clicking noise would happen as my right pedal came up just past bottom dead center but only under slight load. It would not make this noise up on the rack so the only time I could hear it was when I was riding which made it hard to pin point. So each day, after I got home, I would tackle something new on the quest.
First day I put the bike up on the rack and noticed that if I flexed the aluminum fender slight to the right and left it made a clicking sound. It's a sturdy fender and it has 5 attachments to the bike/rear rack including one bolt, down low near the bottom bracket. "Could there be that much frame flex, under load so as to move the fender enough for this to be the problem?" thought I. So I removed the rear wheel and kickstand, loosened the bolt, nut, and all the aluminum spacers, washers and leather washers I have in this area and re-tightened. No noise upon flexing the fender.
Day 2, noise still there. Grrr. Upon this day I removed the cranks, made sure there was no grease where there was not supposed to be and grease where there IS supposed to be. Got out the torque wrench and reinstalled to the correct torque.
Day 3, noise still there. Gah! OK, right hand crank coming off again. All the tiny bolts coming off and the chain rings are coming apart, reassembled with removable threadlocker. Crank reinstalled and torqued again. Tried to remove the bottom bracket but it was in so tight and looked so good I held off.
Day 4, noise still there. What the F? Somewhere in my bicycle repair book I noticed a torque spec for the pedal to crank arms. "Bing!" Pulled out the pedal wrench and tightened the pedals. This took all of TWO minutes.
PROBLEM SOLVED!!! START WITH THE SIMPLE STUFF. I had been switching pedals, off and on, throughout the winter depending on weather I felt like wearing warmer shoes or my clipless bike shoes.