Up until 1.4 if a boat was hit by a stream of water it would rise. This allowed for many builds like water elevators and boat based redstone circuits. See http://www.youtube.com/watch?v=ronO7a_XIvc for an example

As of 1.4 boats hit by a water stream will now glitch down into the ground and disappear. If you cut off the water the boat still will not appear. If you enter the block the boat was in before you hit it with a water stream, it will still be there invisible and will reappear when you collide with it.