I'm the second owner of #288. I really don't think I paid a big premium for mine over a nice '03 or '04 S. This is my dream Boxster. Since these came out I've completely lusted after one. I love the cocoa interior and top, and the solid red tail lights, and the wheels and exhaust tip and blah blah blah. Totally, this is my favorite model Boxster.
Mine also needs a headliner, which I haven't had done yet. I have an IMS Solution, deep sump kit, a ton of other maintenance parts, all ready to go. Actually, I was about to post in the
550 SE thread.
Even though I feel I didn't pay a premium for mine, to answer the original question of are they worth the extra money? I think so. It's a relatively cheap way into a numbered Porsche. They're a bit more special than a regular S, and the folks who know what they are really get excited when they see one.
For me, that cocoa interior alone would have been worth whatever extra it cost!