For those of you who get The Military Channel (it's Ch. 287 on DirecTV), this week is "Sub Week". Every night at 8 p.m. ET/PT, they'll be showing a submarine-themed show, starting tonight with the premiere of "Top Ten Submarines". The 10 "finalists" are shown in this slideshow; while I'm personally inclined to pick the Seawolf-class subs (since those are the ones I know best, having been initial manning Eng on the last two), my guess is that they'll end up putting either USS Nautilus (SSN 571) -- the first "true" submarine -- or the Gato-class boats in the #1 slot. Unless, of course, the slideshow is already in the order they've picked, in which case they incorrectly selected the Type VII U-Boat for the top of the list. While it was undoubtedly an efficient weapon, I don't think that a boat design that had about 80% of its copies lost in combat should be considered the "best" submarine.
Update 0702 06 March: It turns out the slideshow I linked to above does put the subs in their countdown order. It's hard to compare WWII subs to other submarines that haven't been proved in combat -- while the Seawolf-class boats are clearly the "best" submarines in individual combat capability, we'll (hopefully) never find out in actual combat if they live up to their capabilities.