My thoughts: Remove your pedals and grease the threads on the spindle. Also, are these MKS pedals? If so, you may want to try greasing the bearings.

One random notion is that it could be saddle creak. I think I read here on BF or another bike list about someone going mad trying to track down what they thought was a drivetrain-related click, only to find out that it was his saddle. He greased the rails and the clicking went away. Good luck!