I just went through this, so read my story and see if any of it applies: http://www.bikeforums.net/showthread.php?t=58502 I had the same noise, with the pedals in the same position, regardless of gear.

Check:
-front derailleur (as mentioned)
-integrity of chainring teeth and chain
-that crankarms are torqued on tight
-that pedals are in tight; sometimes, if you have a curved crankarm (like the Shimano Octalink) the pedal bushing doesn't sit exactly right on the crankarms surface and you'll get a clicking when you hammer and the crankarm flexes. A quick fix for this is a little lube in between where the bushing meets the crankarm face.
-that the pedals are lubed and the noise isn't coming from a pedal (releasing one pedal and peddling with only one foot is an easy way to test this while riding)
-BB (see my thread above); check for tightness, water, etc.

Good luck.