There isn't a way to put in actual hyperlinks in your message templates. However, if you put a URL in your email template, the majority of email clients out there will render the URL as a clickable link, meaning most if not all of your clients will see it as a hyperlink within the emails they receive.

It's important that the URL is complete, as in starting with http:// or https:// 

You can enter hyperlinks in regular messages (those not from templates) by clicking "Enable Formatting" toward the lower right of the message compose screen.