I personally was a big fan of 688i Hunter-Killer. One of the most realistic sub games ever made, with a 250 page manual that frankly under-explained how a lot of the more technical systems on your boat functioned (I'm still not quite sure when it's a good idea to let out the port/starboard towed arrays!). To get good at the game basically required you to take a crash course in modern submarine warfare.

http://www.stormpowered.com/stormcloud/games/6040/manual.pdf

Man, I really miss these kinds of games. DCS is really all that's left of what used to be an entire genre.