Using internal notes allows you to add instructions thoughts or insight to messages for yourself or your colleagues.
A handy use of the future is to add information to a message and then reassign it to a coworker for follow-up. This improves the speed and overall accuracy of the email coming out of your office by eliminating the need for any one employee to guess or assume about a fact or figure.
It's collaboration and teamwork without ever leaving your desk. You can format the notes with html or hyperlinks if you wish and you can rest assured that notes are always private and never exposed to the customer.