I'm in love with the Type IX boats, especially the IXBs. The other boats have their advantages but I just really feel at home in a Type IXB submarine. I like the feeling of being able to go on extremely long patrols. The IXB is a much bigger boat so you really ARE a captain of a ship.
If I had to use another boat besides the Type IXB, it would be the Type VIIB. That boat is like an athlete; it can do 8 knots underwater, has a steady surface speed, and is very very maneuverable. Looks nice too, like a shark.
Who can go wrong with an IXB? 21 eels, long range, a beautiful ship, and you can stack it up with the IX-3 conning tower for extra protection against nasty airplanes, and more firepower when going head-to-head against other ships. Although I think I'm the only one on this website who is crazy enough to go head-on against warships.
Not exactly submarine captain's behavior, but I haven't found any good naval sims that let you captain a warship yet!