I guess that my problem with trying to give an opinion is that your price point is so wide that even though both cars are Boxsters, they're 'apples and oranges' apart.
I don't know if you're looking at the car as a daily driver or weekend warrior. Both are great cars...I've had two 98's that were not low mileage but were still good solid cars. I'm sure the 06 would be a very nice car as well.
Sorry for not being any help!
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