Recently I wanted to create a new web application in SharePoint and so I went to the Central Admin website to create one, but the option was missing. Even though I was logged in as the System Account, the farm administration account I couldn't see the link. If I navigated directly to /_admin/extendvs.aspx I got an access denied message and none of the accounts configured for SharePoint would allow me access.
So after a lot of head scratching I remembered that I had navigated directly to the administration site directly in an existing browser session and had not used the link from Start Menu. As soon as I navigated from the start menu I realized that I was using Windows Server 2008 and that Central Admin has to be run with administrator privileges.
As soon as the browser opened the 'Create or Extend Web Application' link appeared and all was good again.