It depends on what you want in the car ... (archive)

Though they are both roadster, they are very different cars.
BMW Z3: Powered by smooth inline six engine with lowend torque, it's easy to drive it fast. It handles decent for a roadster too. You have the choice of automatic or manual, it's a great car for topdown cruising with style.
Honda S2000: Follwing the "technology is the replacement for displacement" belief, it's powered by a 9000rpm 4cyl engine. It makes a record setting 120hp per liter, but only 157 lb-ft of total torque(still more than the 3.2L M egine per liter wise). You obtain the power by keep the engine in it's powerband(above 6000 VTEC switch). It handles better than the Z3. It's light weight and has minimal features. It's not meant to be driven in local traffic at 3000rpm below, it's more of a track car.

Thus, there is no which car is a better car sort of judgement, two different cars to serve two different purpose for two different kinda drivers. If you want a more comfortable car that's easy to drive and won't push it to limits, Z3 is the car for you. If you like a sharp edge pure sports car, and enjoy F1 experience type of revving, the S2000 is as close as you can get.

To make it easier, my order of choices(if I can only have one) will be:
new M roadster, current M roadster, S2000, non-M Z3's.
Btw, the S2000 is a great car at msrp, but not if you are paying $38k. Now days most of dealers are selling them at msrp if you place order and wait for the delivery.

If you have more specific questions, I will be more than glad to answer.

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