I am going through the same thing right now. I just bought new OEM rotors and pads, front and rear, from ********************************************************************************************. Cost was $542. Porsche dealer wanted to charge me 1200 EUR~ $1600 to do it. I found an awesome site on doing boxster brakes yourself. Here's the link.
http://www.bombaydigital.com/boxster/projects/brakes/
The guy has step-by-step instructions with color-coded pictures. Idiot proof.
I went with the Zimmerman rotors and Textar pads which are both German manufacturers of OEM parts. I was going to get Pagid pads, but their German sales rep said that for legal purposes, he recommended that I didn't buy their pads because laws here would find me liable in the case of an accident if I had "race" equipment on my car. He said the original type should be more than sufficient for autobahn useage. Also I did not go with the cross drilled and slotted rotors because they wear the pads more by having a "cheese grater" effect. Mechanics I have talked to here said that Germans normally don't turn their rotors, and their rotors as a rule are not designed as meaty as those of American manufacturers; so, I didn't bother to guage the thickness of mine, and just bought new ones. However, the tolerances are listed on that link above in case you want to see if your rotors are still good.
Hope that helps,
Matt