Disclaimer The opinions expressed herein are my own personal opinions and do not represent my employer's view in any way.
With the newer versions of Site Studio (10gR3, at least 10.1.3.3.3+) there is a handy way to set the default link format for your site. You can do this through the Site Studio Designer and the setting is persisted in your Project XML file in Content Server. This is pretty handy if you want to do things like using one manner of linking to data files for 90% of your content creation work.