Document Number: The transaction document number. For example, the check number, the repair order number, the invoice number, the PO number.
Control Number: The transaction control number. For example, on an accounts receivable transaction, the control number is the AR customer number, on a payables transaction the control number is the vendor number, on a car deal it is the stock number, etc.
Reference Number: Transaction reference number. Usually the same as the document number, but can be used as an additional identifier.