Now that the new iPad has been put through its paces, there have been reports that iOS 5.1 is not accurately reporting battery charge percentage. ZDNet has even said the battery algorithm is "busted" while other reports have warned against overcharging the device. For those who are worried about damaging their batteries, rest assured that the iPad is not destroying its own battery.
First of all, every iOS device will report a 100% charge while leaving room to spare. This keeps the lithium-ion batteries optimized. The iPad 3 battery is massive, clocking 42.5-watt-hours compared to the iPad 2's battery at just 25-watt-hours. As a result, iOS may be reporting the new iPad battery as fully charged when in fact it's only at 90% capacity.
According to highly publicized tests run by Ray Soneira, President of DisplayMate, if you remove the iPad 3 from its charger immediately when the device reads 100%, your battery run time is 10.4 hours. Leaving the device to charge for an additional hour or so gives you an extra 1.2 hours of run time, totaling 11.6 hours. Apple vouches for 10 hours of usage on its new iPad official specifications page.
So regardless of whether or not you charge the iPad until it reads 100% on the dot, or keep it plugged in overnight, the device is delivering more than what's promised by Apple. An upcoming firmware update may change how the battery percentage is calculated, to bring the 100% indicator closer to the actual full charge amount. In the meantime, lithium batteries are designed with safety and longevity in mind, so there is no risk in leaving an iPad plugged in after the screen indicates a 100% charge.
iOS lithium battery meters should be reset monthly anyway, by letting the device run down until it powers off, then recharging. For more complete information on maintaining your iPad battery lifespan, see Apple's iPad battery information page.