I need to set access permissions for a user's mailbox and folders on exchange 2007. The powershell cmdlet Set-MailboxFolderPermission is available on exchange 2010 and 2013 and does the job. But that cmdlet is not available on exchange 2007. Does anyone know how to implement the equivalent functionality? There's the interface IExchangeManageStore that seems to work (client-side) but it requires a MAPI profile. It there anything better or easier server-side?

I'd suggest you look at PfDAVAdmin http://blogs.technet.com/b/exchange/archive/2010/04/09/3409758.aspx  and http://blogs.technet.com/b/bill_long/archive/2010/04/07/filtering-output-from-pfdavadmin-or-exfolders.aspx which should work okay on 2007 using the Admin virtual root which gets around need to have client rights on the Mailbox folders themselves. (You can use EWS or MAPI but they will both require you have ether full access the Mailbox or impersonation rights).

Cheers
Glen