A big part of the flagging in Outlook 12 is about forcing the question: When am I going to deal with this? This question is forced when right clicking on the flag column in mail and getting the following menu.
Outlook 12 Flag Menu
Making a selection here marks the mail with a start date and due date and causes the item to appear in the To-Do Bar. Clicking on Custom… gives you the most flexibility – allowing you to set the start date, due date, and reminder. You can also add a custom "follow up" string that appears in the infobar of the mail. This string can be used to remind you of what you were planning on doing with the mail. For example: "Send Thank You note."
Outlook 12 Mail Item with "Send Thank You Note" string