I did a search on "gear noise" and it seems there are lots of theories, mostly revolving around piston slap or other components. My 96 CR500 has what I would call gear noise, like that usually associated with straight-cut gears. The frequency seems too high to be piston slap, but I'm new to either so I don't know. I've got good compression (100 psi at 6,000 feet ASL or 13.5 psig or so in). The bike has always done it (bought used 2 years ago), but I can only hear it near idle (pipe noise overtakes at higher rpms?). The engine is un-molested and unless there was a reason to go into it I'd like to keep it that way.
I am planning on selling it and don't like sayin' "its always sounded like that".