I was wondering if there is any way to enable HTML tags in the emails Indigo sends out? I would like to have email alerts which say for example, "The garage door is open, click here to close it". I can then use the URL from the web interface as the link which will trigger the close button.

No - Indigo only sends text emails.

Some mail clients will automatically turn known strings (i.e. http://XXXX/some/path) into clickable targets - in which case you can just specify the RESTful API URL for closing the garage door in the email.

Yes that works however the URL is very long, could this be something that is added in future versions possibly?

It's already on our request list - but not a very high priority.