I pulled up the linoleum in my bathroom and the sub flooring has water damage. It's pretty thick plywood. How do I pull that up? Its wedged in tight. I have a crowbar and it would be fun to use, but I don't want to ruin anything. The area is only about 5'x5'. It's in three sections. Can I replace the three with one solid piece? Do I put a thinner piece of plywood and then cement board on top of that? If there is plywood under the current piece on top and it's not damaged can I just put cement board on top of that?

This is a more complicated question than you might think. It depends on the size and span of the joists and the size of the tile. You need at least 3/4" plywood under 1/4" backerboard. You can check out the John Bridge Forums for detailed tiling advice.