If you add a little pressure to the shifter (but not enough to engage the gear) for a quarter to half second before moving the shifter into position, you will avoid the clunk. The little knock you hear/feel occurs when the syncro can't work fast enough to equalize the speed between input and output shafts.
When you come to a stop and put the gearbox into neutral, there still may be a few rotating parts inside. The light pressure and slight delay on your part will avoid the clunking.
If you want to hear the syncros at work (and wear them out a bit), let your car coast at about 20 miles per hour in neutral with the clutch IN. VERY slowly try to put the car into first, without actually going all the way and engaging the gear. There will be a bit of resistance as first accompanied with a slight whine that will increase in pitch as you add more pressure. Eventually the whine will subside, the resistance will disapear, and the gear shift will slide into first like butter. Mechanical goodness
