It depends on how you're using your mail. If you are calling the ezmail API directly from in your extension, you can use the setContentType() method on your e-mail instance ( http://pubsvn.ez.no/doxygen/4.0/html/classeZMail.html#ac8ea2b85f149bd38ae1c56b36fdba0b ).
In eZ Publish 4.1.0alpha1 there will also be an enhancement so you can specify the content type inside the template used by the e-mail for certain mails send out by the kernel (subtree notifications, collaboration, tip a friend, user/register, user/forgotpassword): http://issues.ez.no/IssueView.php?Id=11410