Jim
Basically all military aircraft ended up with the combined Luftwaffe and received new serials in the 'western' range.
Most of them never entered service. The MiG-29s and the transports did.
Much of the equipment was sold and/or scrapped while others were portioned out to Museums etc.
All serviceable civil aircraft ended up on the united German civil register.
Some probably failed to receive a valid CofA while others no doubt were sold.
I have not made any study of it, so the above is said from memory with some sweeping statements.
There are books dealing with all Eastern aircraft individual by individual both military and civil, so it should be possible to follow each aircraft and what happened to them.
The Soviet Union's aircraft used by their units based in East Germany were withdrawn to home basis. I believe there were some aircraft left behind, but don't take my word for it...
Cheers
Stig