Heather Solomon has written an excellent article on how to create and use Custom Master Pages for use accross multiple site collections.
One way master pages can be stored and used in MOSS 2007 sites is through creation in SharePoint Designer and storage in the Master Page Gallery. This method will create a master page in the content database. But what if you need to use one or two master page across multiple site collections? For ease of updates and maintenance, we don't necessarily want to store a copy of the master page in each site collection. Instead we can create and store master pages on the file system as a SharePoint Feature and make it available for new and existing site collections.
Complete article is available here.