FWIW, I too will chime in on if you buy a base you'll want an S later. Or do really silly things like spend more money than it is worth putting a larger engine in it.
I bought a low milage (67K) 99 base before I knew more about the 986 line. Had I ov known more, I'd have bought an S.
But doesn't matter if you get a base or an S, a Boxster is a fun car to drive.