I can only speak for the S since that is what I have, but on the street the biggest improvement to braking will be tires. The stock brakes are more than adequate to bring you to a stop and will easily overwhelm the gripping ability of the tires. Whether you go with the OEM pad or aftermarket pad is really more about brake dust and cost. I've used OEM and street compounds from Pagid, Hawk, PBR (cheap) and they all work great on the street with differences in dust and initial bite mainly. I liked the Hawk best all around. (I thought it was the Performance Friction at first, but realized I used them as a track pad. I like Pagids better for the track.)
With rotors, I've used OEM and Zimmerman. The only difference is the coating on the hat for the Zimmerman sucks, so you'll want to to recoat it with hi temp paint unless you don't mind rust. Currently, I'm using Zimmerman rotors, which are cross drilled since I have an S. They are about 2-3 years old with about 20 track days. They've held up really well.
The equation is very different on the track. It's about repeated stopping ability. That's where bigger rotors, cross drilling/slotting, hi temp brake fluid, exotic pads, bigger brakes, etc. become more important to dissipate heat to prevent fade and fluid boiling and maintaining consistency. Adding bigger/grippier tires stresses brakes and so does adding horsepower (because you'll be entering the braking zone faster) and, frankly, just being a better driver (because you'll be entering the braking zone faster

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That said, I'm still using the OEM brakes with Zimmerman OEM placement rotors, ATE fluid and Pagid RS-14 pads (full race compound) with great success. Generally, I "catch up" to others on braking. I was at Buttonwillow yesterday and the only cars out braking me were a GT3 RS with PCCB and a Radical. This was coming from a long straight downshifting from 5th (127 mph) to 2nd (45 mph) (of course they were entering much faster than me). My brakes were solid all day even with doubled up sessions of 40-50 minutes at a time.
I will switch to 2 piece rotors when I need to replace my current rotors--for lower weight mainly and better heat dissipation. I'll keep the existing calipers. If I did an engine swap and picked up another 80 HP, I would likely go with bigger brakes.
I guess my point is that Porsche brakes are fantastic and the mid-engine layout of the Boxster seems to accentuate it further. Spend the money on suspension if you want to go faster. BTW, I was only .3 seconds off the GT3 RS on a track layout that favored high HP cars.