I'm still running the factory hardware on my '03 S with 67k, but I suspect the time is coming sooner than later. I second the bump-stops, they were an issue in my car until replaced.
One of my options is
Koni's FSD setup. Reviews are very good, they seem to have wider capabilities than the factory setup regarding the outer limits of comfort and performance and dare I say they're inexpensive.
The next step in price is likely the ROW (Rest of World (what all Non USA Boxsters got from the factory)) M030. I gather it's harder to find these days and if you do you can add almost $1k to the cost of the Konis.
My final choice would be the Bilstein pss9 coil overs. Thems real money, but the most flexible in their setup capabilities. Hard to say if they can be setup soft enough for some tastes.
Something else to consider is the cost of installation. I've been told the rears in the 986 are no fun to replace, so maybe get some quotes to budget in. When I get mine done, I may also invest in corner balancing. Just a suggestion.