Canned Replies are part of the System Email Pro extension.
A canned reply is convenient boilerplate language you create once, and which is used in a given system email sent to users. For example, you might have canned replies to send to users when a quote is approved, when an invoice is paid, or when a transaction has occurred.
You can read more about how to create canned replies.
Email templates, on the other hand, are built-in to the core Jetpack CRM System Emails functionality. These templates are used to customize the delivery method, subject, and appearance (via HTML) of the system-defined email types.
You can read more about customizing system email templates.
For additional information about customizing email and other available templates, including invoices and quotes, please see our document on editing templates.
Note: The Mail Campaigns extension comes with a built-in WYSIWYG editor for customizing HTML emails sent via Mail Campaigns. This editor is not available to use with the default Jetpack CRM system emails.