HMS Surprise
Several of Patrick O'Brian's Aubrey/Maturin book series
Astrea
Ben Hur by Lew Wallace
The Covenant
Kidnapped by R. L. Stevenson
Ghost
The Sea Wolf by Jack London
Orca
Jaws by Peter Benchley
Hispaniola
Treasure Island by R. L. Stevenson
USS Walrus, Bungo Pete
Run Silent, Run Deep by Edward L. Beach
USS Scorpion
On the Beach by Nevil Shute
Rachel
Moby-Dick by Herman Melville (the rescue ship at the end)
Nellie
Heart of Darkness by Joseph Conrad
The Patna
Lord Jim by Joseph Conrad
The Antelope
Gulliver's Travels by Jonathan Swift
USS Dolphin
Ice Station Zebra by Alistair MacLean
Tsimtsum
Life of Pi by Yann Martel
Jolly Roger
Peter Pan by J. M. Barrie
Dulcibella
The Riddle of the Sands by Erskine Childers
Dawn Treader
The Chronicles of Narnia by C. S. Lewis
SS Carnatic, China, General Grant, Henrietta, Mongolia, Rangoon, Tankadère
Around the World in Eighty Days by Jules Verne
Demeter
Dracula by Bram Stoker
HMS Compass Rose
The Cruel Sea by Nicholas Monsarrat
HMS Bellipotent
Billy Budd, Sailor by Herman Melville
The Nautilus
20,000 Leagues Under the Sea by Jules Verne
Pequod
Moby-Dick by Herman Melville