According to Global Security, North Korea has 22 old Soviet Romeo-class diesel boats, and 4 even older Whiskey-class boats, along with 71 mini-subs. They also have hundreds of small surface ships that could potentially fire torpedoes.
Based on the reported crew size of the South Korean vessel, it could be a Pohang-class corvette that was attacked.
Staying at PD...
Update 1019 26 Mar: According to this report from The Sun (admittedly not the most authoritative source), the ship has now sunk, with dozens reported dead or missing.
Update 1513 26 Mar: The South Korean government is downplaying possible North Korean involvement until they get more information. I suppose it's possible that one of their corvettes had a catastrophic engine room explosion while it just coincidentally happened to be near the Northern Limit line. On the other hand, I'm hearing rumors of more weapons fire at sea. Remember, the ship was attacked on Friday night (their time), and right now it's just before sunrise on Saturday morning, so the entire rescue and investigation has been taking place in the dark.
Update 1528 26 Mar: As I suspected, the sunken ship is reported to be a Pohang-class corvette; it's identified in this article from The Korea Herald as ROKS Cheonan (PCC 772).
Update 1329 27 Mar: Although they don't know yet what caused the sinking, the South Korean government is all but ruling out North Korean involvement.
Going deep...