I stumbled onto a nice list and thought I'd post it up. I realize it includes some already mentioned, but I'm too lazy to edit it.
20,000 Leagues Under The Sea (1916)
20,000 Leagues Under The Sea (1954)
20,000 Leagues Under The Sea (1973)
20,000 Leagues Under The Sea (1985)
20,000 Leagues Under The Sea (1995)
20,000 Leagues Under The Sea (2002)
Above Us the Waves (1955)
Agent Red (2000)
Airboss III: The Payback (1999)
American Heroes: Submarines (2002)
Around the World under the Sea (1966)
Assault on a Queen (1966)
Assault On The Wayne (1971)
Battle of the Coral Sea (1959)
Below (2002)
Captain Nemo and the Underwater City (1969)
Counter Measures (1998)
Crash Dive (1943)
Crash Dive (1996)
Crimson Tide (1995)
Danger Beneath the Sea (2001)
Das Boat (1981)
Deep Shock (2003)
Deepstar Six (1989)
Destination Tokyo (1943)
Devil and the Deep (1932)
Down Periscope (1996)
Fantastic Voyage (1966)
Fer-de-Lance (1974)
Forty-Ninth Parallel (1941)
Full Fathom Five (1990)
Going Under (1990)
Gray Lady Down (1978)
Hell and High Water (1954)
Hell Below (1933)
Hellcats Of The Navy (1957)
Hostile Waters (1997)
Ice Station Zebra (1968)
In Enemy Hands (2004)
K-19 (2002)
Landfall (1949)
Men Without Women (1930)
Morning Departure (1950)
Murphy's War (1971)
Mystery Submarine (1950)
Mystery Submarine (1963)
Octopus (2000)
On the Beach (1959)
Operation Disaster / Morning Departure (1950)
Operation Pacific (1951)
Operation Petticoat (1959)
Out of the Depths (1945)
Run Silent Run Deep (1958)
SeaQuest DSV (1993)
Sub Down (1997)
Submarine (1928)
Submarine 707R (animated) (2004)
Submarine Attack (1954)
Submarine Base (1943)
Submarine Command (1951)
Submarine D-1 (1937)
Submarine Hawk (1992)
Submarine Patrol (1938)
Submarine Raider (1942)
Submarine Seahawk (1958)
Submarine X-1 (1968)
Submerged (2001)
Submerged (2005)
The Abyss (1989)
The Atomic Submarine (1959)
The Bedford Incident (1965)
The Devil and the Deep (1932)
The Enemy Below (1957)
The Fifth Missile (1986)
The Flying Missle (aka The Flying Fish) (1950)
The Frogmen (1951)
The Hunley (1999)
The Hunt For Red October (1990)
The Inside Man (1984)
The Land That Time Forgot (1975)
The Last U-Boat (1990)
The Life Aquatic (2004)
The Mysterious Island 1929)
The Phantom Submarine (1941)
The Rescue (1988)
The Rift (1990)
The Russians are Coming! The Russians are Coming! (1966)
The Silent Service (animated) (1995)
The Spy In Black (1939)
The Spy Who Loved Me (1977)
The Valiant (1962)
Torpedo Alley (1953)
Torpedo Run (1958)
Trapped in a Submarine (1931)
Two-Man Submarine (1944)
U-571 (2000)
U-Boat Prisoner (1944)
Up Periscope (1959)
Voyage To The Bottom Of The Sea (1961)
Voyage To The Bottom Of The Sea (2006)
We Dive at Dawn (1943)
Western Approaches (1944