There are known convertible top issues.
Resources for the Repair and Maintenance of your 2008 Honda S2000
2008 Honda S2000
2008 Honda S2000 Problems
A problem can occur with a vibrating expansion valve in the AC system which causes a whistling noise from the passengers vent. Replacing the expansion valve with an updated valve from Honda should repair this problem.
The S2000 is set up with aggressive alignment settings and soft tire compounds to enhance handling. These alignment settings and soft tire compounds result in tires wearing out earlier than anticipated. This is a compromise made to have a car with exceptional handling characteristics.
Some S2000's can develop a problem with the transmission popping out of fourth gear. A new updated fourth and fifth gear assembly will repair the problem. The transmission will have to be removed and disassembled for this repair.
There is an issue when the ignition switch is on for about four or more hours. The powertrain control module (PCM) can misinterpret serial data and cause the Check Engine Light to illuminate. A software update from Honda will repair this problem.
2008 Honda S2000 Reviews
2008 Honda S2000 CR
Rear tires pretty much go every 10,000 miles even when driving calmly the whole time. The exhaust is not loud at all; in fact, under heavy acceleration, the driver notices engine noise more than exhaust note. The 6-speed manual transmission has to be the greatest shifter put in a production car, south of supercar territory. The cupholders are pretty much useless. I just used them to hold my spare change!
The airconditioner makes weird whistling noises from the passenger side; the trunk is small but relatively big compared to its competitors, such as the Pontiac Solstice or Saturn Sky; the S2000 CR comes with factory tools but no spare tire; the suspension is improved, and if driving a CR and then a base S2000 back-to-back on a track, the driver will definitely have more fun in the CR.
The car could use a bit more power. There are econobox cars, such as the Toyota Camry LE, which can keep up with the S2K on straightlines (not condoning street racing, just making an observation). The factory sound system is rubbish, especially when cruising with the top off. Note: CR comes with removable hardtop, not softop.
Another thing that is a common annoyance with many S2000s is that the car will tell you that the key is still in the ignition even if it isn't when you remove the key to get out of the car. It just continues to make the chiming noise.
I've owned 2 S2000s in the past 3 years. One was a 2007 new formula red; currently own an '08 apex blue pearl CR. The car has its faults just like any other car; however, in the end none of that matters when driving the CR on an open road, enjoying the 100% driver involvement (if you can't drive stick, forget about it!), or just taking it to the track and ripping past cars that cost twice the MSRP of the S! If you buy it, you'll enjoy it. I've daily driven both the S2000s I've owned (traded '07 for '08) and both performed commuting duties flawlessly.