I've owned 2 Boxsters. A '99 and an '01S. Neither was a 20 year old car during my ownership. Both were great cars. Lots of fun.
If I had to pick just on price, a well maintained '98-'99. Record of things like a suspension refresh, oil changes, recent AOS, recent IMS, motor mounts, transmission mounts, etc. From someone who obviously loved the car. Or factor in all those things when figuring the price you are willing to pay.
If I had to pick on value, a '05-'06 because of the improvements made between the 986 and the 987. Many of the same desirables apply with the exception of the IMS.
A list of the changes year to year for the first dozen years of the Boxster is here.
https://sites.google.com/site/mikefocke2/modelyeardifferences