If somehow the path to your masterpage is broken, you will get an error message like "file not found" when you access a website. This could happen if you create a new site from a template, which comes from another server. You can open your site in SharePoint Designer, though.

The KB article A subsite that you create in SharePoint Server 2007 does not inherit master page settings from its parent site, and you receive error messages on the Site Master Page Settings page describes this problem. You can solve it by enabling and disabling the Publishing feature in your sitesettings.