Yup, that's why you need to have world saves. Lots of things can break the server.
Here is the link to bukkits server setup. http://wiki.bukkit.org/Setting_up_a_server
There is a link to an init script which will let you run MC as a service if you want to administer it remotely via ssh. https://github.com/Ahtenus/minecraft-init
I have a cron job setup to call "/etc/init.d/minecraft backup" every other day which will copy the entire world into a backup folder. You can definitely use one of the backup plugins like Roadhog suggested as well. I'd use that in tandem with the init script and then you wouldn't need to setup a cron job for backups.