This is probably the most asked questions related to sharepoint branding and customization. In this post we will discuss how you can change the master page for your site according to some logic like you can change the master page for a logged in user or simply can switch the application.master page to your custom master page for all applictaion pages.

I ahve written a Step-by-step sample code to switch mater page according to logged in user's group. See the Post @ Switch SharePoint master page for logged in user