Oh thank you so much!!!!!
It does not clunk in neutral!!!!
What does that mean now?
A couple of possibilities:
1) The splines on the front yoke/tailshaft are not sufficiently greased and thus are not sliding properly. The scenario would be: as you step on the brakes, the rear axle turns from the braking torque. The leaf springs allow it to turn a bit (the opposite of hard acceleration). This pulls the driveshaft backward just a bit. As you are coming to a stop, the leaf springs start returning the axle to its normal position. The splines are binding so they resist, until they *pop* and slide forward. Putting the trans in neutral takes some of the rotational load off the splines so they don't bind as much.
2) Worn/damaged/improperly fitting splines. Same scenario.
3) Insufficient spline engagement (driveshaft or yoke too short). Splines are not enagaged enough to slide properly, causing them to "cock" a little to the side and bind. Seems less likely that this would be alleviated by braking in neutral.
4) U-joints, as Jim mentioned.
There are certainly more possibilities, including a problem inside the transmission or the transmission mounting (including the crossmember). "Clunking" is a classic symptom of a driveshaft problem so I like to start looking there. All of the other causes people listed will cause clunking, too. The trick is to find a way to eliminate some of those possibilities without spending a fortune replacing everything, and you've got a good clue with the neutral test.