I'll add to what creeperxr7 stated. Chances are most if not all of your bushings are shot. However, if you have your foot on the brake, or the E-brake on for that matter, and shift your car into reverse and it still has the knocking sound and/or feel, then it is your differential bushings and rear mount. These go bad and when they do you will get a "knock" when the car shifts through the gears. It is most evident when shifting into reverse. Your strut rod bushings and lower ball joints will create a "drifting" and "wobbling" feeling when applying the brakes. However, wobbling when you press on the brakes may also be an indication that your rotors are warped. Does your car wobble according to the speed you are traveling? Meaning, when you are going faster, does it wobble faster and when you are much slower is it a slower wobble. If that's the case then you've got warped rotors.
And to clarify what creeperxr7 stated about the strut rod bushings. I've got brand new poly bushings on my '89. I have a very pronounce "knock" when shifting through my gears because my differential mount and bushings are shot. The front suspension will have nothing to do with a "knock" when the tranny shifts gears. It would on a front wheel drive car, but not ours.