Here's my thoughts:
HARDTOP
In my experience you won't use it often. You'd put it on in the winter if you plan on driving your car around in the cold, but if it's rainy/snowy, why would you want to drive the boxster?
18" RIMS (Cayman S type) minimum
Don't waste your time. If you're going to upgrade, get the 19" options.
FLOOR MATS
Yes.
METALLIC PAINT (if I go with silver - how often do Porsche change their colors? Seems like Arctic Silver has been around a while. Think they'll change it up next year?)
Silver is a traditionalist's color. Boring, but high resale value. Get any silver or grey, they're all the same to the next buyer. I recommend Guards Red or Cobalt Blue myself.
19" RIMS (Carrera S) - please describe difference in ride between 17 vs 18 vs 19 without PASM.
Get the Carrera Sport wheels. I will be jealous!!!
PASM
I have PASM. I rarely use the stiff setting. The standard setting is nice, but a bit of body roll in turns. I can't remember what the standard shocks feel like though so I can't compare. I'm happy I have the option though.
One caution--they had to replace my right rear shock already, under warranty of course....
SOUND PLUS vs BOSE
The base system sucks, the Bose system also sucks. You're kind of stuck without any good option in my opinion. The "sub woofer" isn't really sub-bass at all. I'd say save the money and go to Reus Audio, but then you're too far away for that nonsense.
The Bose system isn't musical at all. The bass is one-note and boomy. Sound plus might be the best option if at all, but I suggest test driving both systems. Take the car for a test drive SPECIFICALLY for testing out the stereo, not for anything else, and drive with the top down and top up at speed. Don't just listen on the show room floor or you'll be fooled into thinking the system is actually worth something.
FULL LEATHER
"full leather" seems to mean a lot of different things. At the very least order the basic leather package that gives you the leather trim around the center console and instrument stack, along with the leather dashboard. This is the single biggest mistake I feel I made on ordering my car--it looks SO MUCH BETTER in the leather.
"Full leather", where you get every little bit done in leather is probably a waste of money.
WIND DEFLECTOR
Makes a difference. I feel a lot more wind on my hands on the steering wheel when I don't have the wind deflector in place and the girlfriend's hair goes wild.
I have some further suggestions for you:
Heated seats - worth the money!
Sport steering wheel - I wish I had one, and it's a cheap option. I'd get it!
Short shifter - if you have a passenger, you'll probably be hitting them in the thigh/knee when shifting into fifth or sixth, unless you get the short shifter. Both shift nicely though.
Sport chrono - I have it, it would be the first option I'd leave out next time.
Nav system - Nice, still buggy like the stock stereo though. With the way these things are getting so cheap nowadays, it may be more cost-effective to just get the base stereo system without nav and use all the money you've saved to get a touchscreen nav/DVD system installed with upgraded speakers/amp. That way you'd even get the extra cubby space behind the seats where the stupid Bose "sub-woofer" would otherwise sit.
Sport seats - There's no lumbar support in the standard seats... this is annoying.