There is an email called the "Miscellaneous Charge Email" that has the intention of being in effect an emailed receipt:
This will be sent whenever you make a misc charge against a customer from the customer list.
The email as it now contains the amount they were charged, and also a "memo" field. This field can be filled in for each transaction to give info about the charge and will then be populated into the email, for example:
The email can be customized completely from the Set up page -> Emails and Text Messages > Miscellaneous Charge.