Jobs are stored in msdb. The normal way to delete them is with calls to msdb.dbo.sp_delete_job.

If you have any idea when this occured, you could take a look at agent's log file to see if anything bad happened. It's in a file called SQLAGENT.OUT, in a location like C:\Program Files\Microsoft SQL Server\MSSQL.1\MSSQL\LOG.

The log file gets renamed to SQLAGENT.1,2,3,4 each time you restart agent, so you might see a few there. OUT is the current one.

Another possiblity is someone changed the owner of the job. A non-sa user won't necessarily be able to see other user's jobs.

You can alos take the help of third party MDF recovery software[/url] to recover SQL jobs.