You need to be a little more specific. I will answer from what I have experienced. It seems to me that you are mentioning two separate things:
(1) The thud from teh tranny That is very often worn transmission mounts. Those are cheap and an easy fix. understeer.com even selss metal reinforcements so that there is no movement of the transmission when you shift out of idle. (This whole paragraph will only be good for you if you have a manual transmission -- it would have been nice of you to specify this information)
(2) The lose bearing sound may be from the A/C compressor. Old E36's have this all the time. The A/C will keep working without a problem (mine has been making this sound for all three years that I have owned the car). It is intermittent, because the compressor will shut off and rest for short whiles. To be certain that this is the sound, do two things: (a) let your car idle with the A/C off. See if you get the sound at all. (b) Let the car idle with the A/C on, and listen closely around teh compressor area, which is at the very front of the engine bay, around the lower right corner (right where the A/C belt tensioner is located).
Best of luck. I apologize if I am way off base.