In reply to Jared James:
Depends where /what you want to fish and what your kayak skills are like.
Generally a sit on top gives you much more scope to move around and have tackle and storage that's immediately accessible than a standard touring or sea kayak. They can be cold in winter though. I have both a SOT and a touring kayak fitted out for fishing trips.
Shorter boats are more manouverable and often more stable. I have a fatyak kaafu that works well around bays and rocks but it's slow if you want to paddle a long way.
Longer boats are faster so better suited to offshore marks.
Lots of variables for rod holders varying from simple tubes moulded into the hull through to rail systems that allow multiple accessories each side of the boat. Plastic boats are easy to customise for this and for sonar fishfinders, anchor trolleys etc.
There are also options for pedal propulsion kayaks rather than standard paddles.