Agreeing with JP, if you had different wheel sizes it would make a difference on the feel of the ride. Also, consider the tires that are on each one as condition and quality of your tires will make an impact as well. Honestly, there should be no difference in the feeling of the ride between a regular and S version.
Now here is my opinion on the matter. The standard Boxster is still a fun car, and has a good amount of get up off the line. However, you can generally find an S version for a comparable price in the same condition from what I have seen, especially in todays economy. The S version also has plenty of upgrades that vary from year to year that you will want to compare for yourself and decide if it's worth it. For me personally, my 02 S was worth the bigger engine, painted calipers (vain, I know, but you can't deny!), and other various small improvements that I had to pay only about 2k more for a standard Boxster in the same condition. Finally, I really enjoy having the six speed. Especially for long highway drives, it's nice to pop it into sixth and just sit back and hear your engine purr.
All that said, buy the car which has the features you want and the best condition that you can afford. If the standard Boxster has all you want, by all means save yourself some green. But if you think you will miss some of the features the S provides, do yourself a favor and avoid buyer's remorse down the line.
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