The best advice to give is keep your staff informed on what suspicous actions they should watch for. Obviously as stated above do not use plugins that arn't from BukkitDev. There ARE some good plugins they can be added from other sites then BukkitDev but you will always know Bukkit's Downloads are safe.
As for a DDos attack the best thing you can do is know your server. You lag your server to hell with plugins that Claim they will stop this or do that. But your best method is to know your server and the amount of people it can hold. Then put yourself 5-10 people under your max. This will help for anyone that tries to get all their friends together and bomb your server.
I know I do not have many post but I have been running servers for a very long time and more then just minecraft. Hope it helped,
-Zero