The problem with the Porsche is that once you load it up with options, it gets very expensive. The base price is pretty much stripped.
I looked through the list of options for the 2004 Boxster S at Porsche's website, and here are a list of options that all come standard on the NSX and the amount extra that they cost:
1) CD-changer ($715)
2) Bose Stereo ($1625)
3) power seats ($1550)
4) full leather interior ($2030)
5) Premium Wheels ($1305)
6) HID Headlights ($1090)
7) Chrome Exhaust Pipe ($640)
8) Traction Control System ($1235)
9) Cruise Control ($570)
10) Footwell Lighting ($735)
11) Metal Door Sill Insignia ($425)
12) Floor Mats with Porsche Logo ($320)
---an additional $12k total
So take the $54k base price and add $12k and you get $66k. Now compare that to a new NSX that lists for $89k but is selling for around $80k. And maybe you can get $2k or $3k off a new Boxster -- possibly even less since it is a new model. The price difference is much closer than you would think.