As a summary:
- Files and Wikis have notification templates in XML format at the same time Activities, Bookmarks, Blogs, Communities and Profiles have them as JSPs. That's why customization process is a little bit different, depending of the service.
- But anyway what you can do is: changing look-and-feel of the e-mail, add images, add text with localization support, etc.
- From my point of view, the most interesting thing is that if you want to, for example, add or delete the blog comment author display name or the link for leaving community to/from the notification email template, you can use variables provided by every service! See the complete list of them in the document.