First, you need to determine when exactly the noise is occurring. Here is a series of questions that may point in the right direction:

Is the noise constant? -If not, is it cyclic?

Does the noise occur only when the engine is running? -If so, does shutting off the engine while riding reduce the noise? -If so, does pulling the clutch in (with engine on, then with engine off) affect the noise?

Does the noise occur only when the vehicle is moving?

Does the noise occur only during bumps? -If so, can the noise be reproduced statically (parked)?

Does the noise occur only under certain conditions? -acceleration -braking -engine braking(closing the throttle while riding in gear) -transition from acceleration to braking

Hopefully, these questions will lead you to ask more questions of yourself and hopefully wander in the right direction (this is by no means comprehensive and is meant to be a start to get the page rolling on the wiki).

A stethoscope is useful for tracking down where exactly the noise is coming from, especially engine noise.

Clunks generally mean excessive clearance between parts. For instance, a clunk from an abrupt throttle change at speed might point you to the rear cush drive.

Hissing noises are generally parts scraping/wearing/lacking lubrication.

Cyclic noises (those that repeat periodically) are usually found with rotating parts, such as loose valve/camshaft clearances. With valves, they may disappear/be masked by engine noise at higher RPMs.