I have a Jackson Kilroy fishing yak and love it.
http://jacksonkayak.com/blog/kayak/kilroy/
It is a sit-in kayak decked out for fishing. I like the fact that I am not so exposed to the elements when it is either really sunny or cold.
One thing I was concerned about was the stability and being able to stand and fish. I've found that with this kayak, you are actually standing slightly below the water surface so it is really stable.
Regardless of which one you choose, make sure you get one with a comfortable seat. In my opinion, that is the largest factor to whether you will enjoy fishing from it.