2000 or 2001

[Perfectlap]

The extra power of the 3.2 is handy for highway merging and overtaking slower cars in passing lane. The later 986 S's got a little heavy in weight so the earlier S's are better in this regard. Also, the 3.2 have thicker cylinder walls, an upgrade that didn't make into even the 3.4 996 Carrera -- meanwhile 2.5 Boxsters have probably the most D-chunk failures, particularly those driven lightly. D-chunk failure is nearly non-existent in 3.2 engines. So a IMS dual row S (2000) is probably the best value. Single row IMS S (2001-2004) will cost a bit more to upgrade the IMS if you want the LN Solution kit.
Also, The delta on price is not significant enough to opt for the non-S engines in my opinion. You also get the Carrera brakes, which are the absolute best.