Oooh, been living in RI too long! Anyway, Here are my favorites:
Pure Reference:
U S Submarines since 1945: An illustrated Design History/ Friedman
U S Submarines thru 1945: An Illustrated Design History/ Friedman
Submarines of the Imperial Japanese Navy/ Norman Polmar
The Fleet Submarine in the U S Navy/ John D Alden
Submarines of the Russian & Soviet Navies/ Polmar & Noot
Coffee Table books:
Sharks of Steel/ Kaufman
Silent Chase: Submarines of the United States Navy/Kaufman
Janes Submarines: War beneath the Waves/Hutchinson
United States Submarines (100 years) / David Hinkle
Serving the Silent Service: The Legend of Electric Boat/ J Rodengen
Just plain good reading:
Blind Mans Bluff: The Untold Story of American Submarine Espionage Drew/Sontag
Dark Water: Insider account of the NR-1/ Davis/Vyborny
Rising Tide: The Untold Story of the Soviet Submarines that Fought the Cold War / Gary Weir
U S Submarine Operations in WWII / Theodore Roscoe
How about you U-boat guys? Any good references to add?