The new issue of California Kayaker Magazine (readable online for free at http://www.calkayakermag.com/magazine.html) has an article on boat types that may be worth a read.
In general, kayak fisherman tend toward SOTs. More ability to move around on the boat and access gear all over the boat seems to be the reason. But, you are more exposed to elements with a SOT )and in general, your butt will always be wet), so if you are in cold areas, you may want to consider a SINK as a way to stay warm (or spend more money on appropriate clothing).
Wabakimi Canoe Pack
Electric Kayak Motor
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