First we need to Install Java.

sudo apt-get install openjdk-7-jre

Next lets create a CraftBukkit directory to store all the files.

mkdir ~/mc-bukkit
cd ~/mc-bukkit

And lets download CraftBukkit.

wget "http://dl.bukkit.org/downloads/craftbukkit/get/02389_1.6.4-R2.0/craftbukkit.jar" -O "craftbukkit.jar"

Now lets create a script that we can use to start the Server.

sudo vi /etc/init.d/mcstart.sh

Copy and paste the following text.

#! /bin/sh
# /etc/init.d/mcserver

### BEGIN INIT INFO
# Minecraft CraftBukkit Start script
### END INIT INFO

case "$1" in
  start)
    echo "Starting mcserver"
    MCDIR=$("/home/pi/craftbukkit")
    cd "$MCDIR"
    java -Xmx512M -jar craftbukkit.jar -o true &
;;
  stop)
    echo "Stopping mcserver"
    kill `pgrep mcserver`
    ;;
  *)
    echo "Usage: /etc/init.d/mcserver {start|stop}"
    exit 1
    ;;
esac
exit 0

Now lets make the file executable.

chmod +x mcstart.sh

And launch

sudo /etc/init.d/mcstart.sh

The first lunch will take a long time so be patient.

If you want to start CraftBukkit when your Pi boots up then run the following command.

sudo /etc/init.d/mcstart.sh start