Apart from the Peleus affair (U-852, Eck), the Kriegsmarine fought an unusually honourable war in my view. Of all the services in WWII, of all major combatant nations, the KM stands out as a service with an excellent record.
I of course do not consider submarine warfare "mean", "cowardly" or "vicious" at all. To me it is an accepted form of warfare, and all nations practiced it with varying degrees of effort and success.
If you can read German, perhaps you'd like to read this site:
http://www.wlb-stuttgart.de/seekrieg...fbruechige.htm. It's about alleged and proven war crimes on the seas. The Peleus is the only German offence that can be proven. The U-247 and U-516 incidents were not proven to be crimes despite eyewitness testimonies in the latter's (and presumably in the former's as well) case. Uboat.net doesn't list Matschulat and Wiebe as having done anything out of the ordinary. It seems that in both cases survivors were killed by gunfire, but not specifically aimed at - which must have happened all the time of course.
Kind regards,
Eichenlaub