I use whitelist, but when it kicks non-whitelisted people, it just says your not whitelisted. Is there any way to make it say "You need to apply to play on this server at (Website)!"
You'll need to get a sperate whitelist plugin to do that, as the default one does not offer that feature. There are many on BukkitDev and the forums, just search BukkitDev for Whitelist and you should be able to find one. http://dev.bukkit.org/server-mods/?search=whitelist