Generally speaking I'm going to say 2000-2002. First, I don't think IMS is a reason to rule out one 986 over another because we've had a way of addressing this flaw for some time now. IMS is a non-issue if you are willing to pay for the upgrade. But the IMS may be a reason to favor one year over another.

That being said, 97-99 is nimble and light but with the introduction of the S motor you'll get you more power and not much of a bump in curb weight.
The extra power is handy when merging on highway on-ramps and overtaking pick ups and SUV's hogging the passing lane.
These 3.2 engines also have stronger cylinder walls so far fewer D-chunk failures. The 2003-2004 have a mode of engine failure that is unique to those years and not seen on the 2000-2002 engines. Simply one less thing to worry about engine wise. The 03-04 extras like the glass window can be added to a 2000-2002 in the aftermarket and after 10-15 years that top needs to be replaced sooner or later anyway. If you can land a dual row S model from 2000 that's probably the best since the LNE bearing will last longer than single row LNE bearing for 2001-2004. Also, you'll pay less for low mileage 2000-2002 S than a low mileage 2003-2004 S which is a win in my book because as far as performance and "cosmetics" the 2000-2004 Boxster S is essentially the same car.

2000 S with a dual row IMS for the win. Which just so happens to be what I have. :)

Curious, what is this?

"The 2003-2004 have a mode of engine failure that is unique to those years and not seen on the 2000-2002 engines"

I shouldn't have stated it that way. It's not unique but much more common. According to J. Raby, the 03-04's have a more prevalent issue of destroying lifters and cams than the 2000-2002 due to unique changes to the lifter carrier made on these 3 chain engines.

I've got a rare 2001 Boxster S with a dual-row IMS :D

Confirmed by pulling the OEM bearing out.

Not that rare. We see 01 S cars with dual row bearings all the time.