My '03 GS500 has developed an interesting problem (I'm reasonably sure this started at some point during the last 1000km). Whenever the bike is moving/rolling and the throttle is at idle (or "zero", I suppose), an intermittent clicking noise emanates from the gearbox. All gears are selectable, no issue with false neutrals. The sound only occurs when the bike is actually moving, and cracking the throttle open just a millimeter makes the sound stop. The sound does *not* occur when first gear is selected. Any idea what could be going on?

With or without clutch engaged?

Are you saying you are in gear with the engine at idle and letting the bike roll at it's natural pace?

Could just be chain noise from it relaxing and getting taken up in quick succession when the bike's pace slows down and speeds up compared to the engine (putting torque on and removing torque from the chainring).  Could just need the chain tensioned.

Could also be the same thing but with the gears in the transmission.  There could be a small amount of play and is audible when you transition from engine giving power to wheels slowing engine down.

http://gstwins.com/gsboard/index.php?topic=64709

Clean and grease the splines on the O/P shaft.

Minor update: the noise does indeed also occur in first gear, but very faintly. Also, to clarify: the noise isn't a constant clicking, it's a short series of clicks followed by quiet followed by more clicks. In other words, it's not click-click-click-click-click-click-click-click, but click-click-click-*two or three seconds*- click-click-*2-3 seconds*-click-click-click.