I'm very new to the Minecraft community and have been dabbling in Minecraft server hosting the last few weeks. I currently have a server running on a small Amazon EC2 instance, but it doesn't take much to hit 95+% CPU. From what I've read, this is primarily due to the heavy amount of disk reads. I've tried running the server from a RAM drive, but the server still eats through the CPU. If the world data format is the issue, is Bukkit flexible enough to revamp the way the server reads/writes data to ease the CPU stress?
I think one of the next major updates of Minecraft will contain a new world save format anyway, exactly to resolve those issues.
