What are you interested in?
Roman amphitheatre: Pula,
Roman palace and ruins: Split
Medieval towns: Dubrovnik, Korcula, Hvar, Split, Trogir, Sibenik, Rab, Rovinj, Porec
Sandy beaches: Lopud, Lumbarda (Korcula), Partizanka (Hvar), Lopar (Rab) and others: www.croatia-beaches.com/sandy
National parks, waterfalls: Plitvice, Krka (near Sibenik)
"Venitian" architecture: the whole coast
"Austro-Hungarian" architecture: Zagreb and the small towns in Slavonia (close to the Hungarian border)
By far the most relaxing way to visit Croatia are trips by ferry. There are two weekly ferries going down from Rijeka up to Split - Dubrovnik - Bari (Italy). Between Split and Bari, they run almost daily (3 different companies). There are also daily ferry crossings from Ancona and Pescara in Italy to Split and some Islands.
The most popular Islands are Korcula, Hvar and Rab, where tourists mainly concentrate in the "capitals" with the same name. Less frequented places are Lastovo, Mljet, Brac (except Bol), Vis, Pag, Susak, Ilovik, etc.
Have a look at the following sites: croatiatraveller.com, dubrovnik-online.com, korculainfo.com, lastovotravel.com, lopud.eu, jadrolinija.hr,
krilo.hr/raspored_en.htm, lariveralines.com, losinjplov.hr/veze.htm