Enabling the application mode to set whether CRM can be opened in a browser window without menu, navigation and command bars.
Once we enable the Application mode there is small difference in using the URL.
When we use just organization name without page name it is working, like http://servername/orgname
If we use URL with page name like http://servername/orgname/main.aspx it is opening inside of the browser.
Even we enable the application mode if we do not use the proper URL we may not be able to see the effect.