Lots of people post the same question and the most common answers contain:
"Buy the best maintained, newest S model you can afford, and have a PPI done."
"The least expensive Porsche you buy will be the most expensive car..."
In concept, I understand and agree with them, but the question that
you need to answer is "Who are you, and why do you want the car?"
I have more than one Boxster, but my daily driver is a 1999 with the Tiptronic transmission. With basic care, it is a great car for it's age; it's comfortable, reasonably economical, fun to drive, and it's a Porsche. While there are many enthusiasts in online forums discussing modifications and the best oil, there are also many thousands of owners who just drive them. Happily.
The following threads give another perspective on Boxster ownership from Retroman1969. He bought a 1999 Tiptronic Boxster with the intention of putting a lot of miles on it as a daily driver. Over two years he put more than 50,000 miles on it and chronicled the problems and work that he had done to it:
http://986forum.com/forums/boxster-general-discussions/54957-bought-beater-boxster.html
http://986forum.com/forums/boxster-general-discussions/59827-hyper-daily-driver-one-year-later.html
http://986forum.com/forums/boxster-general-discussions/61228-big-test-repairs-long-route-66-ghost-town-trip.html
...there's more if you search for Retroman1969's posts. When the car "died", I bought it from him and did some maintenance and minor repairs (A few hundred $ in parts and my own labor). I put another 1,500 miles on it, kept the brand new top, and sold the car for about $1,000 more than I paid for it. I recently saw the car for sale again for about twice what I sold it for.
The S model is a great enthusiast's car, but for a reliable and affordable Porsche, I'd consider a 1999 base model.