For example, the custom field with tag "myfield" does not appear correctly in the subscribe notification email when [[custom_myfield]] appears in the notification email copy.
This is a known issue with a workaround. Instead of the custom field's tag, you need to use the ID number of the custom field as a workaround for now. View your custom field list and hover over one of the options in the "actions" column for a custom field. In your browser's status bar, you will see the id number in the URL. Use this in your notification email:
...replacing "12" in the above example with the id number of the field.
Note that the id number is not always the same as the "#" column of the custom field list although it sometimes is.