DutchSubmarines.com
This is THE resource for Dutch submarine information.
Ron Martini
Probably the site with the most links to other submarine pages. Large book selection too.
Submarine Central
Very complete page with lot of pictures
Submariners Association
British submarine site
Submarine Sailor
SubmarineSailor.Com, a site dedicated to helping submarine sailors and their families stay in touch, and preserve some of our history along the way. 
SubSim Review
Site with reviews, hints & tip, news etc. of submarine simulators. 
Neal Stevens' Deep Domain (This image © Copyright 1997 Neal Stevens; trademark registered - do not copy.)
Neal Stevens' Deep Domain
Very nice submarine site. 
BritSub
A Reference of British Submarines from 1901 to the present day.
SUBNET
Where you'll find just about everything you've ever wanted to see and read about the U.S. Naval Submarine Force ... the "Silent Service.
U-boat.net 
Find the German submarines in WWII.
Submarine Graphics
A lot of submarine related graphics.
Electric Boat

This is the company that builds America's submarines. For 100 years Electric Boat has held the reputation as the  world's leading designer and builder of submarines. 
The saga of the submarine
A short history of the submarine
SUB.net It@lia
Italian submarine site. Has a database of Italian and foreign boats.Nice!
Steel in the Deep
Very cool Japanese web site. Has a lot of submarine sounds and a large links section.
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The U-boat Archive
This web site was created to make the records and photographs of the U-boat War available to those who want to learn more about the battle between Germany's U-boats and the Allied anti-submarine forces that opposed them during World War II
Nuclear Submarines Undergoing SRP
(Ship/Submarine Recycling Program)  at Puget Sound Naval Shipyard, Bremerton Washington.
Royal Australian Navy
Nice picture sequence of a torpedo hit
Turkish Submarines
Good site about submarines of the Turkish Navy, site maintained by Ömer Kalaycýoðlu 
Submarines Covers
A collection of submarine pictures and covers (postcards with stamps) by Ronny Saxe. 

No idea what his word means but it belongs to a fantastic Russian web site about submarines. Lots of pictures of old and current submarines and also a section with model submarines. Site is in the Russian language. 
kriegsmarine.net
Web site about the German submarines in the WWII period (1935-1945) by Lawrence Paterson
PSUBS.COM
Great site about personal submarines to promote and encourage the discussion, design, construction, certification, ownership and use of Personal Submersibles. 

Parts Geek
Website with history and parts of the submarine.