Thumper nailed it, try a few or read a heck of a lot on line before purchasing...
I got the Wilderness Systems, Tarpon 120 Angler, which is a sit on top yak with a ton of storage in it. I like it a lot because I sit higher in it than I would in a cockpit type kayak, it is very stable, and easy to maneuver. I didn't really try a lot of Kayaks before I bought mine, I did however read a lot of user reviews on line for a lot of Kayaks and this one was rated pretty highly by a lot of end users. There are Kayaks that do more, have more options etc, but not in the price range that I bought. Sit on top yaks are generally heavier than are cockpit type boats, but they usually do offer more storage, and do allow the user to sit higher on the water which helps if you plan on fly fishing from it.
If I had it to do over again, I would make the same buying decision that I made but I may opt for a different color. Mine is Olive and I would probably go with a beige or lighter color. come down to the store sometime and take a look at what we have and learn a lot from most of the people there that have kayaks, and what they like about the type that they have. Obviously, both types (sit-on-top, and cockpit) are popular and you will find folks that argue one side or the other, so as you listen to what they have to say, keep in mind what you want your yak to do for you and what you expect from it