I'm pretty sure it runs on Spigot, which from my understanding is like a customized version of Bukkit that improves performance and stability. (I may be very wrong here...so just wait for replies from more technologically informed people before you rely on my answer. )
EMC runs on Spigot which is an advanced version of CraftBukkit. It has much improved performance and stability as Kadboy said. Though technically we run on EMC CraftBukkit because Aikar has done some of his own code modifications. It's on Github somewhere.