After going missing over 60 years ago, the US submarine Wahoo (SS-238) has been found between Hokkaido (Japan) and Sakhlin (Russia) islands.  She's laying at a bit over 200 ft.

Commisioned in 1942, this Gato-class fleet submarine completed six highly successful patrols, the last four, plus the fatal seventh patrol, under the command of Cmdr. Dudley "Mush" Morton.  She was one of the most highly decorated US submarines of WWII, with her and her crew earning six battle stars and a Presidential Unit Citation. 

Here are a couple of articles describing a bit more:

Missing WW-II submarine located - United Press Intl

Navy confirms discovery of sub Wahoo - Honolulu Adv.

USS Wahoo - Navsource Online

And a good telling of her story at:
USS Wahoo - Wikipedia.org

The Polish navy has released sonar images of what may be the wreck of the Graf Zeppelin, a large German aircraft carrier sunk at the end of WWII.  The wreck was recently (July 2006) found by Polish oil company divers.

  Der Spiegel sonar article...

  Original Spiegel article...

Remains of a Japanese mini submarine may have been found north of Sydney Harbour in 20 meters of water.  The sub, known as M24, was one of three which attacked Sydney on May 31, 1942.  The other two subs were recovered from the bottom of the harbour as the crews had killed themselves after failing to escape.  The location of the third sub had been unknown.

  Herald Sun article...

A midget submarine is a small submarine, typically with a one or two person crew and with no on-board living accommodation. Midget submarines normally work with mother ships from which they are launched and recovered, and which provide living accommodation for the crew and other support...