Documentation for JIRA 4.0. Documentation for other versions of JIRA is available too.

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-Dmail.debug=(true|false) — will enable/disable SMTP mail debugging (but note this will only work in 3.7.2+).
-Djira.jelly.on=(true|false) — will enable/disable Jelly scripting
-Datlassian.mail.fetchdisabled=(true|false) — will enable/disable mail fetching services for IMAP and POP
-Datlassian.mail.senddisabled=(true|false) — will enable/disable JIRA sending mail
-Djira.trackback.senddisabled=(true|false) — will enable/disable trackback linking
-Djira.i18n.texthighlight=(true|false) — will show text elements of JIRA that are internationalised