Miatas are great cars - I owned my 97 M Edition for 5 years. Great handling, good brakes, so-so torque. Cheap to own, cheap to fix. A bargain.
The Boxster is faster, cooler, more expensive to buy, own, and repair. If I've got the money, I'll take the Box - but I agree with BruceLee, it's not really a straight line comparison. Hopefully the car that costs twice as much is better. Whether it's worth the difference is each individual's call.
BUT HERE"S MY GRIPE ON THE 2006 MX-5!!! They put in the new z-fold top, thereby seeming to eliminate any chance of putting in an SCCA rollbar to track the car! What's with that???? Miatas made their reputation on tracks across America, and the Mazda stiffs the enthusiasts. WTF? (stands for "what there for?" keep a clean site
)
I have thought of getting another 1.8 and setting it up for track only. The NAs are cheap enough to do it. Save the Box for cruising.