To get the existing settings

Get-MailboxAutoReplyConfiguration “username”

To set the Out of Office (internal and external)

Set-MailboxAutoReplyConfiguration -identity “username” -AutoReplyState enabled -EndTime 08/11/2011 -InternalMessage “username will be out of the office from Friday 21st October until Tuesday 8th saving the world.” -ExternalMessage “username will be out of the office from Friday 21st October until Tuesday 8th saving the world.” 

To disable Out of Office/Auto Reply

Set-MailboxAutoReplyConfiguration “username” -AutoReplyState disabled

To disable Out of Office/Auto Reply and clear the Internal/External message

Set-MailboxAutoReplyConfiguration -identity “username” -AutoReplyState disabled -InternalMessage “” -ExternalMessage “”