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Since from Joomla! 1.5 was introduced the concept of overriding core layouts using the template override system. Template overrides are a good method for changing the way Joomla shows component and module output without changing the core Joomla system code. That's important because it means that as Joomla is upgraded to new versions you will not have to repeat the changes you made.
Read more on Understanding Output Overrides
The official how to
Joomla! version 1.6 introduces some a set of features on Layout Overrides in Joomla