I've been researching for IHW: Pigboats, my WWII submarine RPG. One of the things I am doing is re-reading old WWII Submarine novels, and seeking out and buying more to read. I want to get the atmosphere right! WWII submarine novels? Don't laugh! It used to be a fairly popular sub-genre. The first one was Run Silent, Run Deep by Edward Beach, which was a huge commercial and critical success back in the fifties.Beach was the Marryat (http://en.wikipedia.org/wiki/Marryat) of the genre. Like Marryat, Beach was the thing he wrote about. He was a submarine officer throughout the war, ending up in command of the Piper, which reached the Sea of Japan just as the war ended. RS,RD is excellent - great characters, and wonderful action. I first read it in the early sixties, along with the two sequels, Dust on the Sea and Cold is the Sea, neither of which were as good as the original, though they were good.
Harry Homewood wrote three WWII submarine novels in the 80s - Final Harbor, Silent Sea, and O God of Battles. I have read the first two, and they are excellent. Silent Sea is a sort of side sequel to final harbor, as the protagonist is a fairly important character in the previous book. Real seeming characters, awesome action, and complex, yet organic, plots. They are highly recommended! Homewood was a WWII submariner himself, though not an officer. Post-war, he ended up as a newsman- bureau chief for Newsweek, Editorial writer for the Chicago sun times, etc. These books were very popular when they were written, but are pretty much unknown nowadays - unjustly, in my opinion.
J. T. McDaniel is a modern writer of the genre, and Bacalao is a great book. It is apparently his first novel, though he has been published as a submarine fact writer. The book has a charming flow to it, and lots of technical detail. Again, wonderful characters that work together marvelously. this is really typical of WWII submarine novels - they are very much character driven.
Another currently active writer is R. Cameron Cooke, who was, like Beach, a submarine officer who retired and began writing. His two WWII books are both very very good - Rise to Victory, and the sequel, Sink the Shigure. I think his plots and his characters are not up to the previous writers I mentioned above, but maybe a notch below them. Still very well written.
Some other books I am exploring but have yet to read are Halsey Clark's 5 book "Sweeping Saga" the Periscope series, Claude Pearson's Gunfish, and Charles Rush's Battle Downunder.