Because of security and performance reasons we, among other parties, prefer to have no HTML comments created by any plugins. WP Super Cache creates numerous of these.
So far we've edited the plugin code manually to remove these, but that's not update-safe and is beyond most siteadmins to start with. There are also other plugins to do strip all HTML comments before the final HTML is sent, but that adds its own resource footprint and a new possible avenue of security issues.
Would you be kind enough to add an option to disable the outputting of any HTML comments? It could be called eg. "Show debug information in HTML comments" and be checked by default, and us security- and performance-minded would just uncheck it.