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...

The title tells most of the story.  The wrecks are from a British transport fleet that was sunk in an attempt to block a French bombardment.  Interesting.  The ships were discovered in 2005 and just announced now (spring 2006). 

Here's the article:

 livescience.com Article...

No good, definitive news yet in search for USS Aligator prototype (Alligator Junior).  Searchers used a magnetometer to scan a suspected mound along a tributary of the Delaware River but the results indicated a smaller mass of metal that was expected.

  Philadelphia Inquirer article...

A replica whaling ship, the Carthaginian, was recently sunk off the Maui coast.  It landed upright on the sandy bottom in 95 feet of water about a half mile offshore of this popular Hawaiian island.  The hope is that this wreck will attract marine life and provide an interesting destination for scuba divers and underwater tourists aboard Atlantis' tourist submarine that operates along the Maui coast.

  Press release...

I just put up a menu link to the Submarine Wreck Map which is an original Sub-Log feature.  This is another version of the Shipwreck Map and it's very similar but displays only submarine wrecks.  (About 1200 submarine wrecks listed.) It also has a couple of nice features:  you can easily search a specific area of the world and limit a search to wrecks of a specific country.

Like the Shipwreck Map this one isn't working well with Internet Explorer.  Please give it a try with Firefox though!  And post any comments to the Wreck Maps forum.

Update: it's mostly working with Internet Explorer now - the Search Radius circle isn't being drawn but everything else works.

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...

Local volunteers, NOAA and the Office of Naval Research are all abuzz about a mound found near Rancocas Creek in Riverside, Pennsylvania.  The hope is that it may contain the remains of a submarine, the prototype of the USS Alligator.  The US Navy, while not the owner of this prototype sub, may assist with a ground penetrating radar to evaluate the possible wreck site.

  Courier Post Online article...

Divernet magazine is the online version of Diver magazine and they have some great material.  My favorites are the Wreck Tours and there are currently 79 of them!  Each tour is a page or two of text and illustrations describing a wreck and a dive on it.  I really appreciate the hand drawings of the wrecks.  They do a good job of showing the overall layout of the wreck - much more than a photo or two can do in most water. 

Here are links to the two sub wrecks that they describe:
UC-70

HMS Umpire

And check out the whole list:
Divernet Wreck Tours