I really like my S2K. I just got the E90 to replace an '02 Maxima (VQ35 6MT) which I do like (it's for sale). When I bought the S2000, I found that the overall balance of the Maxima wouldn't do it for me, and I missed RWD every time I jumped into the Honda. There are a lot of S2000 drivers who drive BMWs for this very reason. I do miss the torque of the VQ35 whenever I drive the S2K/325, but that's the only thing I miss.
I think the S2000 is an absolute bargain. If you are looking for a GT car, the 350Z/G35C would be for you, but they are fat pigs when compared to the Honda. Mine's 6y old already, and the structure is just as firm as new. There is no cowl shake, the engine sings like new, the suspension is original, the leather is in great shape... basically, the car can be beaten and with a little bit of maintenance it won't let you down. As far as handling is concerned, I don't think it can be topped. The AP1s ('00-'03) have a tendency to snap oversteer, but I have found the back end to be very easy to control. IMO Boxster S > Z4M > S2K > Boxster > Z4 3.0 > 350Z convertible. It is true that you have to wind it out to get someplace fast, but there is 9K to play with. My wife and I took a 3500 km trip to the west coast and it was a great car for the mountains. To top it off, we got 36 mpg (imp) on the trip.
2006 325i - Sparkling Graphite
2000 S2000 - New Formula Red
2007 Chev Silverado crew cab Z71