Owned both a base '99 and an '01S. While there was a numerical difference, I actually preferred the 2.5 litre 201hp '99 over the 3.2 litre 250hp '01S. The '00-'03 base are 2.7 and 228hp.
Of all those, the '03 in any form has a few conveniences and the glass rear window which can be important in colder climates.
Model year differences and some write-ups on buying a Boxster are
here.