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Here are the major differences that haven't really been mentioned here.
As Car and Driver stated, the S2000 is more at home on the racetrack, meaning the handling is much crisper and the ride is stiffer.
The 350Z is a much better touring car, i.e. more luxury options, more comfortable on the highway, better trip car, etc...
I own an S2000 but have test driven the Z and they are both great cars in their own right. You just have to decide what it is that you want in a car and go from there. Chances are, if you decide on the Z, you will, at times wish you had an S, and vice versa. Either decision will be a good one.
what everybody said was on the mark... it comes down to wither you want a comfy daily driver... or a car that can really make you blow your load on the track... both are awesome choices, I love the 350z and I own a s2000, if I had the choice.. I would get a G35 as my daily driver, and on the weekends, just drive the S for fun... forget bout the lack of torq... don't worry about it, you can get gear ratioing's for that... once again, either way is a great choice, but if you want a fun car... you got to go with the s2000... hehe, good luck deciding!
I too considered a 350Z. I test drove both. I liked the overall handling of the S and the fact that it is a convertable. If you wait till the 350Z convertable comes out, expect to pay a nasty premium making it cost $10,000. more than the S. What would you do if you had $10,000. in your pocket? The S is by far the better value and choice. Good luck in your choice!
I personally like the 350Z. I think it looks very sharp, and if you add nice wheels to the 350Z it will look outrageous. But I love my S2000! It has everything I ever wanted in a car {Fast, Convertible, Great looks}. Here a some pictures that can help you decide.
I have an S, my best friend has a Z, they're both great, and both fast. Car and Driver got faster numbers (.1 sec) with the S. Road and Track favored the S on the road, the Z on the track. The Z is more practical though. More trunk room, more interior amenities, more head room, leg room etc. The S I personally think is more fun to drive, it feels like a sports car. you should read the car and driver "racy roadster" article and the road and track article (it's in the issue with 0-100 on the cover). They really give good comparisons.
You guys keep comparing the Road & Track tested 350Z to the S. Don't forget, it was the convertible 350Z that was tested and not the track version of the Z, which is supposed to be a great handling car. However, I've always wanted a true roadster and felt then as I do now that the S is the best out there for the money. Plus, I'm not all that crazy about the Z, convertible or coupe.