If the noise stops when you press the clutch, then it's definitely the tranny. Hmm, rod knock noise from the tranny... I'd have to say it's a missing tooth, or something along those lines. I've had bad input bearings make a 'shhhhhh' noise that I could turn on/off with the clutch pedal, but no knock sounds.

If it's rod knock, the sound at idle is uneven. cl, cl, cl clack, clack, cl, clack, etc. Reving it in neutral should net you a consistent stream of clacks.

If it's coming from the tranny and the problem is on the input shaft side, then it will match engine revs (as long as the clutch is out).

I don't have a lot of first hand experience with rod knock, but if you put in really thick oil (20W50 or something) wouldn't that change the sound of the rod knock? And on that line of though, wouldn't that change in sound (or no change) be a pretty good indicator if a knocking sound was coming from the bearings?