Opus: That's pretty easy because I drove them both for the last 6mos. On one day: 2hr up/back switching cars with my wife.
I love the 997. The room is most welcome even tho' my wife is 5-4 and I'm a normalish 6-0/190lbs. The lack of a spare tire and the missing extra trunk are comparative negatives. The mass is noticable but the torque available is thrilling. The 997 is not as pretty as the 986 but very handsome. Yes about the 'S'. Even tho' I have no interest in racing or much into speed for that matter, I like the upgrades ...and feel they also come into play when it comes time to find the car a new home.
The Boxster by contrast is clearly more organic. You much more feel as if you are driving the car vs. directing it. You can feel and hear the 986 better - perhaps that small space for the jumpseats in the 997 makes a difference or there's more sound proofing. (this may also be what 993 people are saying; tho' I've never been in one..) The 986 - even with the std. shifter - shifts diffferently. It seems you need to be more direct whereas the 997 is smoother but more vague. I will not miss the convertible top. I kitesurf 2-3 times a week, so I get plenty of 'outside' and Maryland tends to get hot/humid, so the AC comes on anyway. Understand that all this is a comparison between a 2001 986 and a 2005 997, so I assume the newer Boxster has numerous upgrades besides the 03's backwindow. I did not consider a Cayman - simply did not appeal to me.
The big question is why I would spend about 2+ times the money simply to replace something in the garage that we (my wife drives them as much as I ...tho' she feels more conspicuous in the 997) only drive a few thousand miles per year where the differences are quite small? Well, when you carry no personal or business debt: you have options. The 997 is an option ... as the 986 was a couple of years ago. Cheers.
Jim