Player,
I am not aware of detailed TROMS (Tabulated Record of Movements) for German merchant ships although they may exist somewhere on the web.
Frankly, the Germans conducted most of the war over the land mass of Europe and with few overseas territories and the dominance of the allied navies, there was little call for troop ships per se. The exception probably being the reinforcing of Italian troops in North Africa.
However, those liners that did exist, e.g. Cap Arcona, Wilhelm Gustloff etc were used during the war as accommodation ships, destroyer/sub tenders and were only really called into service towards the end of the war when large numbers of troops were being pushed back to the Baltic coast by the Soviet armies.
This resulted in the few ships available to carry out an effective evacuation being significantly overloaded with terrible loss of life.
Fuller details can be found here:-
http://en.wikipedia.org/wiki/List_of_Kr ... roop_shipsJim S