I had a 2003 S2000 as well as a 2006 and 2007 S2000. The Boxster is just a different car. Much better low end grunt, better ride without sacrificing performance, quicker, faster, handling more neutral, fit and finish comparable (both are to a high standard in my opinion). What the Honda has over the Boxster is value. You can buy a brand new 2008 S2000 for $33,000 out the door, and the Boxster will depreciate in value by that much in 5 years. But quite frankly, the Boxster is a superior car, and I really care more about what the car does day to day than the value tomorrow.
vincesf