A clunky transmission can be caused be a couple of things.

Most common from my findings is that the torque arm between engine and swingarm axle is worn out, allowing the engine to twist in the frame.

Worn engine mounting rubbers can also allow the engine to move around a little, but the stock Honda rubbers are pretty good. HRC supplied more rigid rubber mounts, which work well and doesn't cause any undue vibration.

Bent shifter forks can also cause things to go a little clunky.

Old or low oil (as Dave pointed out) certainly wouldn't help either.