Documentation for JIRA 4.3. Documentation for other versions of JIRA is available too. 
Excel templates of reports are controlled by the file \secure\views\browser\report-excel.jsp. While you can't easily have different report-excel.jsp for each report, you can easily edit the report-excel.jsp file to behave differently for each report (or if you want, use a different include for each report).
The report-excel.jsp has full access to methods available in com.atlassian.jira.web.action.browser.ConfigureReport. This means that you can figure out what report it is from the getReportKey() and
getReport() methods, and make the page behave accordingly.
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