Heather Soloman goes through on how to create master page(s) on the web server that appear in the Master Page settings for a site collection for the Collaboration Portal or Publishing Portal site templates. This will be useful if your requirements entail using one or a few master pages for several site collections and you need to not create multiple versions of the master page in various content databases. This allows you to create a single master page, use as many times as you like, and update it in one single location on the web server. Here is a snippet:

Open your new site and change the master page the site uses:

1. Go to Site Actions - Site Settings - Modify All Site Settings - Master page (under the Look and Feel submenu)
2. Depending on your requirements, in either or both the Site Master Page setting and the System Master Page setting, select your drop down box and choose your custom master page.
   

Click How to Create and Store Master Pages on the Server for Use with Site Collections for the original article.