Burning Bridges said:
I believe there were a few cases in the Pacific, but I highly doubt that the survivors would have been left for days in rafts, facing sharks on their own.
There is the AHS Centaur, a Australian Hospital ship sunk by a Japanese sub, 64 survivors (out of 332) and 36 hours until rescue, the SS Junyō Maru sunk by the HMS Tradewind British submarine with 723 survivors (out of 6343) but the Junyō Maru was a Hell Ship, it was carrying POW and Javanese slave labourers and also the SS Montevideo Maru sunk by the American sub USS Sturgeon when carrying POWs with 18 survivors out of (1140), all survivors were crew.
In Europe you have the MV Wilhelm Gustloff, German Hospital ship sunk in the Baltic by a Soviet sub S-13 estimated 9400 dead, 1252 survivors (largest loss of life on a maritime disaster), the SS General von Steuben, also sunk by the S-13 with about 300 survivors (out of of 4267) and the MV Goya sunk by the Soviet sub L-3 (minelayer submarine) with 183 survivors (out of 7000).
Those are the only incidents concerning submarines, with aircraft there is more, SS Cap Arcona (German), SS Thielbek (German), RMS Laconia (British, already mentioned), HMT Rohna (British) and the SS Armenia (Soviet).
Of course listing all civilian transport ships sunk in WWII would take a long time, the only ships sunk by U-boats seem to be the SS Athenia, SS Arandora Star, SS City of Benares, RMS Lady Hawkins, SS Caribou and SS Leopoldville besides the already mentioned incident.