Documentation for JIRA 4.0. Documentation for other versions of JIRA is available too.
JIRA generates emails in reaction to events using a templating engine. The templating engine is Apache Jakarta's Velocity. This is a relatively easy to use templating language that can pull apart java objects in useful ways. The mails are generated inside JIRA by invoking Velocity with a set of objects of relevance to the event.
To customise email content, please follow this procedure.
atlassian-jira\WEB-INF\classes\templates\email
jira\src\etc\java\templates\email
webapp\WEB-INF\classes\templates\email
See also Adding Custom Fields to Email.