That's a tough one... I guess I have several favorite boats.
The Type VII[b] is what I've used the most, so I'm most comfortable with it. The torpedo stores can run out pretty quickly, but the deck gun is there for a reason. It's also fast, and agile as far as submarines go, and it's just generally well rounded. Take care of her and she will take care of you, as they say.
But for all out fun, the Type XXI scores 100/100 in my book. About 18 knots submerged top speed, an entire hovercraft's worth of eels, and gigantic batteries plus schnorkel means lots of happy times. Oh, and homing torpedoes.
Too bad it only arrives on the scene in 1944... But yeah, it spoils you pretty fast. Any earlier and the game would turn into a turkey shoot. Still, anytime I just want to unwind, nothing beats an Elektroboot!