Here's my mystery: My !990 RS gives me this little knock when I use the engine to brake, and then again when I accelerate. It sounds like it's coming from the back, so I thought it was the rear axle, or some of the gears in it. I asked the guy at auto zone, and he said it was probably the crush differential. I asked my hanes manual, and it said it might be some loose nuts, and that I should go and tighten them. Any thoughts as to what it might be?

 

I'd remove the tranny mount and see if it's broken.

 

I can almost promise you its one of 2 parts or related parts, your torque arm is disconnected or broken somehow and hitting the trans tunnel, or the trans isn't bolted to the x-member, or like above, x-member is broke.
On a less severe and equally likely note, still dealing with the TA and x-member, bushings could be shot, a likely example is that the TA chewed through its bushing and now has some play in it and hits the metal bracket it sits in everytime you accel or decel.

So check the following for breakage/wear/loose/disconnected:
torque arm, torque arm bushing, torque arm bracket(where it mounts at the trans), torque arm bolts at the differential, trans crossmember, trans xmember bolts and bushings.

 

If none of that, could be the U joints in the DS.