The world data, which also includes player inventories, is saved to a folder in the current working directory of the server.

The level-name setting of server.properties determines the name of the folder, which defaults to world. This setting can be easily changed to create a new environment and toggle between saves.

Vanilla server commands related to saving/backups:

/save–all - forces the server saving. /save–off disables saving. This should be performed before you create a backup of a running server. This will prevent the server from saving while you are copying, which can lead to a corrupt backup. /save-on - re-enables saving.

Thank you! I hadn't thought to disable saving while creating a backup. - aedia l Jun 22, 2011 at 14:27

i saved the server to my desktop so were will the directory be?? - user14851 Nov 20, 2011, at 8:22

Do you know if it is possible to run the saveoff and save-on commands using a batch job? - mpontillo Apr 26, 2012 at 14:53

@Mike If you are looking for an automated way of backing up, you might consider plugins such as Bukkit Backup and other Bukkit backup plugins. I would also recommend mcrcon, which allows remote commands to be run. Schism Sep 8, 2012, 19:23

There should be a folder called "world" in the directory that you are running the server. There are all files that your server will need to run in that directory. The most important thing to backup would be the region folder within the world folder, which actually contains all the "block information". The world directory also contains the players folder. This folder stores information about the players that have connected (inventories, etc.). Strongcraft (Note: The directory is named world only if the level-name property in server.properties has not been changed.

This information applies to a Vanilla or a Bukkit multiplayer Server.

TL;DR: backup the entire world directory.