This seems to come up a few times.  The following sample script in PS applies a common master page across all SPWebs in a site collection.

$site = Get-SPSite http://fba.contosotest.com/dv1
$site | Get-SPWeb -limit all | ForEach-Object { $_.MasterUrl = "/dv1/_catalogs/masterpage/custom_v4.master";$_.Update() }
$site.Dispose()

 

Thanks to Phil Childs - http://get-spscripts.com/2010/09/changing-master-page-on-sharepoint.html