What's this noise? Is it from my crank?
I've had similar problems (clicking on the right side down stroke) before, and it is probably the bottom bracket.  But the first thing to do is to check and make sure that you don't have a loose bolt/ nut somewhere.  This could be in your pedal, the crank, or somewhere else in your drivetrain.  If you make sure that everything is tight and it still doesn't go away it's time to try replacing your bottom bracket.  It's a pretty easy fix, but does require a special tool.  http://sheldonbrown.com/tooltips/cartridge.html