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Magento Version: 1.5.0.1
I’m not sure when this feature was added. It’s there in 1.5.0.1 and might be in previous version.
The phtml template file for your system emails are located in
app/locale/en_US/template/email/
However, you don’t want to edit these files. Instead, go to
System -> Transactional Emails
This UI will let you create a copy of the email in the Admin Console.
Then, if you go to
System -> Configuration
Each email has a config option somewhere that will let you choose a template. For example
System -> Configuration -> Email a Friend -> Select Email Template
This is a perfect place to use my free System Config Search extension.