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SQL Server Backup. Because SharePoint stores most of its information in SQL Server, you can use SQL Server backup tools to back up most of its information, including the configuration and administration databases. You can also use those backups to restore the databases, but it's not supported. Given the synchronization issue, it would seem that as long as you make sure to synchronize what you're restoring then it should work just fine. The key thing is to ensure that no configuration changes are made during your backup window. However, you'll still be missing any customization information stored in the file system if this is the method you choose to back up SharePoint.
Because SQL Server backup tools can be run from the command line, you can schedule this to run at convenient times using Scheduled Tasks. It does require that you manually reattach your databases to the appropriate Web application after a recovery.
What it can't do is back up the search database, and for an odd reason: the search indexes aren't stored in SQL Server. Because you can't synchronize the search database after a database-only backup, this backup approach isn't a viable option for that database.
Windows Server 2008 Backup. The native backup and recovery system for Windows Server 2008 can be used to back up all those things that aren't in the databases (such as the configuration and customization files), but it can't be used to back up the databases themselves.
It seems that the native tools have as many limitations as they have benefits, but it's possible to create a "workable" solution if all you have are the native tools -- especially if you can do a regular shutdown of your farm. If you do a shutdown, you could do a SQL Server backup of all of the databases to a file system that's then backed up using the Windows Server 2008 backup system, along with the directories where customization and configuration information is stored.
Third-party SharePoint backup options
Obviously, to properly back up SharePoint, you need to back up all databases and some files in the file system, and you need to guarantee that these various backups are synchronized. A good recovery system would also allow you to restore the entire system, all configuration and customization data, as well as all content. In addition, it should be able to restore any of the above to various points in time, including the ability to recover individual pieces of content, such as a document.
This was first published in June 2010