We left our boat in Croatia for the winter in 2001/02.
Have a look at my website - link below. You will find two reports on Croatia, one for 2001 and the other for 2002 as well as my Passage reports for the years in question. The Croatia 2001 report contains a specific section on overwintering.
I would recommend Zadar: it is well-protected from all winds, pretty well-equipped and a great base to start from. To arrive/get away, probably the easiest is this: bus to Trieste bus station, bus from Trieste bus station to Trieste airport, Ryanair flight to Stansted.
Dubrovnik also has a good marina.