I've got an iPad 2 and never have run it down to "empty." Been searching around for what others recommend and find conflicting ideas. The first link suggests running the battery down completely until shutdown every so often and the second link warns against running down the battery any lower than 15%.
My 14 month old iPad 2 has never been run below 25% and is plugged in to the charge cord every single night regardless of the battery level without any ill effect. I still get over eight hours with around 25% left.