The Boxster and S2000 are both cars that I have in my sights. I have not yet had an opportunity to drive either but from all reports, both are excellent drivers cars.
When comparing the same model years, the S2000 should be available at a lower price than the Boxster and IMHO it would be the better bet from a maintenance/reliability perspective. There is also the cool factor in how Honda managed to get 240hp out of a 2.0/2.2L engine. The revving character of this engine and the light stiff responsive chassis makes me think the S2000 would be like driving the automotive equivalent of a sport bike. The more traditional front engine layout is preferable for maintenance/repairs and large Honda dealer network is also a bonus.
However, while both are purported to be great cars on the track, my impression is that the Boxster would be more comfortable/forgiving as a daily driver. In addition, with the front & rear trunk space it would be suitable as a touring car for weekend trips etc. I also think the flat 6 would be a more flexible engine for normal driving...and it makes beautiful noises. I prefer the styling of the Boxster, and I must be honest, there is some appeal to owning a Porsche.
Tough call... I'll take both please.

I'd love to hear the thoughts of those who have driven both these cars.