The Gotengo ("Roaring Heaven"), also known in the West as Atragon, is a fictional submarine battleship that has appeared in several tokusatsu films of Toho Company, Ltd., beginning with Atragon in 1963. The model consists of 19 pages of colored parts of which most are very tiny.
Gotengo Papercraft

Five submarines from Total Annihilation are up for download. There's Shark, Snake and Leviathan of Cora and Arm's Lurker and Piranha submarines.
Total Annihilation - Submarine Papercraft

A papercraft replica of the Walrus-class submarine currently in operation in the Royal Netherlands Navy.
Royal Netherlands Navy Walrus-class Submarine Papercraft

A 1:500 model of the fictitious modified Typhoon class submarine from the Tom Clancy novel The Hunt for Red October and the Red October film.
Red October Submarine Papercraft

A model based on the Sub Marine Explorer, a submersible built between 1863 and 1866 by Julius H. Kroehl and Ariel Patterson for the purpose of harvesting oysters and pearls in the Pearl Islands.
Sub Marine Explorer Steampunk Submarine Papercraft

The Type D Koryu is a midget submarine with crew of 5 used by the Imperial Japanese navy in the World War II.
Type D Koryu Midget Submarine Papercraft

A 1:100 scale papercraft of the U-boat Type VIIC, a German class of submarines commissioned between 1940 and 1945.
U-boat Type VIIC Submarine Papercraft

A bigger and more detailed papercraft of the manned research submersible owned and run by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). this 1:35 scaled Shinkai was designed by Rizky. A smaller version can also be found here.
1:35 Shinkai 6500 Papercraft

Total Annihilation - Arm Construction Submarine Papercraft

Alvin (DSV-2) is a manned deep-ocean research submersible owned by the United States Navy and operated by the Woods Hole Oceanographic Institution (WHOI).

Alvin Submersible Papercraft

ZRP's version of Captain Nemo's Nautilus from Jules Verne's classic science fiction novel Twenty Thousand Leagues Under the Sea that was published in 1870.
Captain Nemo's Nautilus Papercraft

Mir (Russian for world or peace) is a self-propelled Deep Submergence Vehicle used for scientific research and submarine rescue operations. The MIR submersible can dive to a maximum depth of 6,000 meters (19,685 ft).

MIR-2 Submersible Vehicle Papercraft

The Shinkai 2000 is a manned research submersible capable of carrying three people up to a maximum depths of 2000 meters.
Shinkai 2000 Papercraft

The Shinkai 6500 which was completed in 1990 is a manned research submersible that can dive up to a depth of 6,500 m. It is owned and run by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) and it is launched from the support vessel Yokosuka.
Shinkai 6500 Papercraft

Deepsea Challenger (DCV 1) is a deep-diving submersible designed to reach the bottom of Challenger Deep, the deepest known point on Earth. On March 26, 2012, this craft was piloted by the renowned Canadian film director James Cameron who became the first person to reach Challenger Deep in a one-man craft.

Deepsea Challenger Sub Papercraft

Check out Tekzo's 1:35 model of the The single-seat Hydra submarine used by Heinz Kruger to escape in the Captain America: First Avenger film.

Captain America - Hydra Submarine Papercraft

Das Boot which is the German for "The Boat" is a 1981 German epic war film written and directed by Wolfgang Petersen. Set during World War II, the film tells the fictional story of U-96 and its crew. Another excellent model from uhu02. Just be warned though that there are lots of tiny parts that new modelers might find difficult to assemble.
Das Boot U96 Papercraft

The "SMG Enrico Toti" was a Toti Class Italian submarine which first sailed on September 14, 1933 under the command of Lieutenant Commander Albert Battle. It reached the Red Sea via the Suez Canal and sailed around Africa and back to the Mediterranean through the Strait of Gibraltar. The submarine is retired and now part of the museum in Milan.
SMG Enrico Toti - Italian Submarine Papercraft via PR

Proteus is a submarine from the 1966 science fiction film Fantastic Voyage. In the movie, the Proteus was miniaturized and was injected to Bene to destroy a clot.
Fantastic Voyage: Proteus Papercraft

The Titan Terror Fish is a submarine disguised as a fish. It is the nemesis of Stingray in the Stingray tv show, a children's marionette television show that aired from 1964-65.
Stingray: Titan's Terror fish Papercraft