I have gone through and added HTML templates/emails for each of the template files in the CP Home -> Email Notification Templates but not all of them are being sent as HTML. I don't know what else I need to change. The Admin notifications are coming through as HTML and some of the others are as well.
For example, the 'Forgotten Password Instructions' comes through as HTML, but the 'Mailing List Activation Instructions' will not.
I have changed the variables in the Email class to be 'html' for mailtype.
There is nothing different between the emails except for the variables.
v2.5.5 - Build Date: 20121220