Silent Hunter III
Dangerous Waters
The Naval Combat Pack (Old games but good ones),
Fighting Steel
You can get these games right here in the Subsim Store
http://www.subsim.com/store.html
Harpoon Comander's Edition
http://www.matrixgames.com/games/game.asp?gid=325
or Harpoon 3 Advanced Naval Warfare
http://www.matrixgames.com/games/game.asp?gid=325
(If you want a simpler interface, go with Comander's Edition)
War Plan Orange
http://www.matrixgames.com/games/game.asp?gid=326
Pacific War: Matrix Edition: A free, updated old game from way back in the dos days but it's still a fantastic game. I play it every once in a while.
http://www.matrixgames.com/games/game.asp?gid=235
Distant Guns (Storm Eagle Studios) or the Distant Guns: Jutland that they are coming out with (These are WWI naval action).
http://www.stormeaglestudios.com/public/home.html
Global Conflict Blue (It's free and pretty damn good)
http://gcblue.com/wiki/index.php/Main_Page