It is a black vehicle that allows batman to traverse the waters. It completely hydro powered, having no need to surface. It is complete with a crime lab, food supply, weaponry, and on-board computer system that can connect with the Batcave's server system and allow batman to upload holographic images.
In Batman Forever, Robin is allowed to use the Batboat while Batman takes to the sky during the assault on The Riddler's HQ. Unfortunately, The Riddler and Two-Face had rigged the sea with mines, using a "battleships" style way of attempting to destroy the Batboat. Eventually Two-face managed to trigger the correct mine, to which The riddler exclaimed "you sunk my battleship!" leading to the destruction of the Batboat.
Fortunately, due to an escape-pod, Robin remains alive and ready to face his families killer.
Batman Arkham City
The Batboat made a quick appearance in Batman: Arkham City #2 - Breaking Ground, when one of the supply boats in Arkham Asylum had been stolen, and it would be flagged to Batman if any veichles left the island. After getting the notification, he went to take his water scooter, and next to it was the batboat.