It's very difficult for me to choose my favorite German thrash band, although if nailed down, I would probably go with Kreator. On their earliest albums, the band employed two singers. It was not until Mille Petrozza officially took over the helm that they truly became a great band. Their early material was great, but Mille's songs were always the highlights because of his shrieking vocals. Pleasure to Kill is one of the greatest metal albums of all time, much less thrash albums. Unfortunately Kreator went through a little dry spell in the mid to late 1990's. However, they came roaring back in the 2000's. "Enemy of God" is a great newer thrash metal song. Recently they have been incorporating some melodeath influences, but recent album Hordes of Chaos is still a great release.
Sodom is the most consistent of the German thrash bands. Unlike Kreator or Destruction, there really was no period of time when they were not putting out consistently good music. Early Sodom is often considered one of the forebears of death and black metal. When they became a straight thrash metal band, they put out amazing album after amazing album, such as Agent Orange, Persecution Mania, and Tapping the Vein. Even now, they still put out consistently good and memorable albums, even though re-recording their first EP may not have been the most popular move.
Honestly, my least favorite of the three German bands, but certainly a great band nonetheless. Destruction's vocalist Schmier is similar to Mille Petrozza of Kreator in delivery, but not as effective. The ultimate thing that sets Destruction apart from the other two bands is the guitar riffs. Destruction has been blessed with some amazingly creative guitarists. Much like the other two bands, Destruction is still going strong. D.E.V.O.L.U.T.I.O.N., released in 2008, was a very strong album.
Another German thrash metal band that has captured my interest and which will probably be discussed at length in the future is Holy Moses.
At the end of the day, Kreator has the best singer, Sodom the best songs, and Destruction the best riffs.