I was wondering about this, too. Lately it seems like I have a lot of rattle idling in neutral, or really any time the clutch is released. I replaced the clutch in February, and made sure I topped off the fluid(but I did use some off-brand standard Dexron/Mercon ATF). The best way to describe it is a light rattling, but very noticeable. The car also makes a humming noise if I downshift while rolling(before letting the clutch out...it's like an ascending hum, I would believe it's synchros spinning up the selected gear before I release the clutch). It shifts smooth, and makes no serious knocking noises or anything. Just the rattle.
I read in a very old back issue of Road & Track(I think it was March, of '91) where they did a test of one of our cars, and the testers noted 'gear rattle at idle', it was stated in the article that it was the 'new' rod-shifted tranny. Any thoughts on this?