Jake is right.
I"ve owned and modified quite a few cars over my lifetime. Some I modded "lightly"...a couple I put WAY too much money into. My boxster is a car I intend to modify "barely" - as like you said, I think most of it is just about perfect out of the box...
one observation I have come away with is that while engine modifications seem to make VERY minimal gains on normally aspirated cars - the same does not hold true with regard to suspension mods.
If you have a 99 boxster with standard suspension and 17" wheels - adding 18" wheels (if they fit), and stiffening up suspension by adding coilovers, sway bars, of the OEM M030 upgrade package - WILL make a substantial difference in handling that you WILL feel. the "bang for the buck" for some suspension mods is huge depending on how your car is setup from the factory.
some of the small cosmetic mods, add no power, but will greatly change the look of your car - if that stuff is important to you. painted bumperettes, for example, are not *that* expensive, and on some color cars - makes a dramatic improvement in the look of the rear end of the car.
one small and relatively inexpensive mod that I also did, which I am happy to have done, was the upgrade the shifter console to the newer 987 one. I paid all of $167 for it, and installed it myself. shift throws are a bit shorter, and much tighter/firmer. I'm sure the $350 short shift version woudl have been better - but if you are trying to be like me - and get the MOST bang out of the LEAST buck, and ONLY mod stuff that really makes a differnce, then this was a great little mod.
if I was going to suggest mods that won't break your bank but will make your car more fun to drive or "nicer to look at", I'd suggest:
paint the bumperettes
987 shifter console
upgrade tail lights and side markets to the 03+ units - you can get these for not too much.
03+ headlights - these are more $$$$ than the tails. if you get litronics it's $$$
desnorkel - free. sounds a bit throatier.
M030 suspension upgrade and 18" wheels. you could probably find the M030 setup fro under $1000. the wheels and tires are not cheap..tires alone will be $1000 for good ones..give or take...and the wheels, if you don't already have 18s, are not cheap. i might suggest looking at some of the knock off wheels...some are very nice and priced right.
when you are dealing with older cars like ours, it becomes silly and counter intuitive to invest too much money into fixin the car up. my car, like yours, is an older one. i have a 2000 base. if you are like me and paid in the neighborhood of 10-12k for your car - spending $2500 on an exhaust system seems like overakill.
spending $176 for a shifter that actually makes it more fun to drive the car - I can live with that.
if I"m going to dump $2500 on an exhaust, I"d rather save that $2500 and just buy a newer/faster/better Porsche to start with. if you are buying an older boxster, you are likely a "budget" minded enthusiast.... the mods I suggested would likely be stuff you woudl enjoy.... good luck.