The best WWII sub-sim overall (IMHO) is Silent Hunter: Commander's Edition. Based in the Pacific, you play as an American sub skipper against the Japs. It has a fully dynamic campaign game that never plays the same way twice. It was made in 1996, but the graphics and gameplay are amazing. I still have this game on my harddrive. If you can find this game buy it.
Second best is Command Aces of the Deep: A WWII sub-sim based in the Atlantic. You play as a German sub skipper against the Allies. It also has a dynamic campaign, but the graphics aren't as good as Silent Hunter. Yet, it does have great gameplay. This game is available as a FREE DOWNLOAD from the Home of the Underdogs site in the "Simulations" section. The only caveat is that the game won't work if you have a Soundblaster Sound card.
Hope this helps
