Don't forget

• 1931's Seas Beneath
• 1943's Crash Dive. Oscar winner for special effects.
• 1954's Disney 20,000 Leagues Under the Sea with Kirk Douglas and Peter Lorre. Oscar winner for special effects, art direction. (There's a 1916 silent version, too).
• 1957's The Enemy Below. Oscar winner for special effects.
• 1958's Run Silent, Run Deep with Clark Gable and Burt Lancaster.
• 1959's Operation Petticoat with Cary Grant and Tony Cutis.
• 1966's Fantastic Voyage with Raquel Welch - 'nuff said. Oscar winner for special effects, art direction.
• 1995's Crimson Tide with Gene Hackman and Denzel Washington. Grammy winner for Best Instrumental Composition Written for a Motion Picture or for Television.
• 1996's Down Periscope with Kelsey Grammer - 'nuff said there too.
• 2000's U-571

jbird added a few more:

• Submarine Command (1952)
• The Man from Atlantis (1977)
• Deep Blue Sea (1999) - While not technically about submarines, it takes place at an abandoned submarine base
• The Hunley (1999) - A TV movie based on the first submarine that was launched during the American Civil War

A sub also features in the plot of 1992's Under Siege w/ Steven Seagal, and they pop up in several James Bond films.

And on TV:

• 1964's Voyage to the Bottom of the Sea
• Star Trek episode Balance of Terror (TOS) is a redressed Run Silent, Run Deep.
• 1977's Operation Petticoat
• 1993's SeaQuest DSV