The best upgrade hands down were excellent tires. The previous owner had these Continentals on the 17" stockers.
I went with Toyo RA-1's on 18" Carrera lights. Holy Cow. it was like a different car.
I was making up excuses to drive it. At the first autocross I remember thinking "even a monkey could probably drive this car fast".
A Boxster on mediocre tires is still good though. That's how good the car is out of the box.
Which makes options kind of pointless. However that didnt' stop me from putting in GT3 seats and Fabspeed headers/exhaust.
worst option (value wise) was to put in Litronic headlights. I spent $1400 (now probably a bargain price) and it was pure vanity. The car didnt' move any faster and it was all about looking up to date.
Best cheap mod was $80 for PORSCHE door decals. Totally reversible. Took all of 30 minutes to put on. When I added the 997 Turbo replicas a few people asked if I traded in for a new car.