Merchant ships

28 Oct, 1940 Empress of Britain (42.348 GRT)
a steam passenger ship sunk by U-32 (Jenisch)

Warships

25 Nov, 1941 HMS Barham (04) (31.100 tons)
a battleship sunk by U-331 (Tiesenhausen)

and more:

http://uboat.net/special/biggest.htm

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Karl Donitz recieved 10 years (or 20 ) at Nuremberg because of the sinking of merchant vessels.

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"Es gibt keine verzweifelten Lagen, es gibt nur verzweifelte Menschen". ----
There are no desperate situations, there are only desperate people. - Panzer General Heinz Guderian

What I found was that he served 10 years of an 11.5 year sentance for doing the same thing that the Americans did in the Pacific. The verdict had controversy associated with it as the American Naval officers recognized they did the same thing. This may go to illustrate that the post-war trials are more about punishing the loser than serving justice.

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PEOPLE SLEEP PEACEABLY IN THEIR BEDS AT NIGHT ONLY BECAUSE ROUGH MEN STAND READY TO DO VIOLENCE ON THEIR BEHALF. GEORGE ORWELL