Current Japanese car magazines are discussing what a model year 2010 S2000 might look like, and have produced a speculative sketch: 
In my opinion, the sketch simply expresses current Honda styling trends, and certainly did not originate from Honda. Furthermore, the styling elements are a couple of years old, and Honda's design language will have advanced by then. Look at the upcoming NSX for the aggressive creases and angles that will define Honda performance cars going forward. You'll note, too, that the sketch includes provision for a folding hardtop (note the A-pillars), which has also been speculated on for the past several months. That supports the generally accepted theory that the car will compete against the Miata with a wider range of options and configurations.
2010 is probably too soon for the next S2000 - we would have seen spy shots of the car being tested by now. The next S2000 is not likely to be a simple restyle, since it will have to meet Honda's own ACE standards for pedestrian and occupant safety. That would require significant changes from the current car, including a higher hood and wider body.
With Honda's limited performance program resources focused on the new NSX, the 2012 timeframe seems more reasonable. The majority of Honda's technical resources are by necessity focused on perfecting new "green" technology for several different cars scheduled to appear over the next few years. So I would believe that the NSX engineers are probably being moved over to the S2000 program as they finish different stages of the NSX program. The NSX, as the Nurburgring photos demonstrate, has already finalized it's engineering and is well into the test phase. I'd expect a final engineering freeze later this year, tuning and test to complete next summer, and that means production 12 months later for the mid-2010 model year at the earliest (remember that the NSX has a brand-new engine and drivetrain).
The article in the Japanese press also mentions a ~286 HP 2.4 liter engine as well as a 3.5 liter V-6 for the next S2000. I find this disappointing (both are low-rev engines of no interest to enthusiasts), but it does support earlier speculation of both a Honda (4 cylinder) and an Acura (6 cylinder) variant of the basic product. Personally, I think that Honda's 4 cylinder engines are technically dated, and that their SOHC V-6 engine family is seriously dated. Both need a much more sophisticated valvetrain with independently variable camshaft timing, rather than the dependent phasing they use now. And they need direct injection, which is state of the art technology, and which would help with much-needed low-end torque as well as with mileage and emissions.
The Acura 2.3 liter turbo engine is the worst example of this entire issue. It produces limited HP and torque for it's size, and is known for it's terrible mileage. Compare this engine against comparable competitive 4-cylinder engines such as the GM 2 liter turbo (260/260 hp/torque) and the Mazda 2.3 MazdaSpeed (274/280) - with both engines growing to 300/xxx over the next two years. And note that the GM Turbo 2 liter gets better EPA mileage in the Solstice/Sky in direct-injected Turbo form than it does in port-injected naturally-aspirated form.
So while Honda leads the world in fuel-cell technology, I'd argue that their "big" (2 liter and up) gasoline engines are falling rapidly behind the curve. I'd hope for a remedy in this area to appear at the same time as the next S2000, and for the most prominent example of that engine to be be featured in the S2000 as it was in the original S2000 in 1999.
