I too have been looking at this a bit. There are three or four common choices, all about $800 by the time you get it all done. I am looking at
http://softronicsoftware.com/
The big thing with the normally aspirated Boxster engines is how little there is to be gained with the stock setup. Another way of stating this is the Porsche squeezed about as much as they felt comfortable with at the factory. Generic out the box tunes can really only get about 5-8 hp without stepping into a risk space the responsible tuners are not comfortable with. Many other engines I have owned previously can safely be dialed up 25-50hp with minimal risk and so this is a bit of a surprise to most 986 owners.
Reduced pulley conversions get about the same gain, an expensive exhaust might get 5-10 in the real world. Other tweaks and mods perhaps 5 hp real world. More than that you have to look at major mods to the engine internals and consequently possible reduced reliability or drivability under anything other than race conditions.
For this reason, there seems little appetite among many 986 owners to go this route. Instead some wait until they have done all the engine mods they are going to do and then get a custom tune at a dyno center to wring out everything available for that custom setup. At a reputable shop and you are placing all you trust in the ability of the tuner. Good ones know their stuff, bad ones wreck engines. Even if I wanted to go this route the population density in my part of the country would necessitate a very long drive to entrust my engine to a tuner with specific experience of a 986 and a hard earned reputation to maintain.
I might take another contributors suggestion and put the cost towards driving lessons once my engine is back to factory output. That should be worth more than 5-10 hp.