Uncle Fuzzy was inspired by a suggestion for a Pearl Harbor map in which one of our young friends asked about Japanese midget subs. So, in a burst of curiosity, Uncle Fuzzy did some research and found a few good links on Japanese midget subs.
This is a page from the University of Hawaii, describing their find of a Japanese Type A sub, which was sunk by the USS Ward.
Interestingly enough, the commander of Pearl Harbor, as well as Admiral Kimmel, CinC of the Pacific fleet, disregarded warnings of the midget subs' sightings (the Ward sank one before the aerial attack.) These were launched by an I-class mother submarine.
One, the Ha-19, had a malfunctioning gyroscope and ran aground on Oahu; it was captured, and its pilot was the first Japanese PoW in American hands in WWII. Better luck next time, buddy!
The nice people at the US Navy have more pictures for us of Japanese subs from later in the war. At this point, the A, B and C types were replaced by the Koryu type sub.
Also interesting are the Kaiten (Skate?) suicide subs; generally 4-5 of these were launched by motherships. They were crude constructions, designed to allow a pilot to blow himself and a 3,000 pound warhead up. Combinedfleet.com has a good account of the sinking of the USS Underhill by one of these:
There was actually quite a large piece of shown about those in the Discovery show: Unsolved History: Myths of Pearl Harbor.