I did the same price comparisons recently. For me, it basically came down to the fact that if you wanted the power windows and locks, then the Sahara made more sense - it was cheaper. At the time I didn't think I cared about the better radio, but now that I have it I realize it would have been a mistake not to get it.
I actually ended up buying used, because a nice 08 Sahara optioned exactly the way I would have ordered one came available locally with low miles. I wouldn't have ordered the dual top, but again, now that I have it I have to say that I really like the Sunrider.
And I definitely second the idea of getting the 3.73 gears if you get a 6-speed. I have no idea what is best with the auto.