The fallen Transformers referred to in the title "Revenge of the Fallen"? It helps to answer the question when it is pointed out that the actual title is "Revenge of The Fallen," not "the fallen," but "The Fallen." The Fallen mentioned in the title is a singular Transformer (although Megatron does come back).
In the begining of Cybertron, Primus created thirteen transforming autonomous robotic organisms. These were the thirteen original Transformers. They were all Primes, and all guardians of something. Soon after he was created, the guardian of entropy, the aging and dissolution of order in this universe as presage to a new creation, he became obsessed with the dark side of entropy. He betrayed Primus and chose to worship a new god who awas more suited to his interests: Unicron. But Primus was not unaware of this. As punishment for betraying him, Primus took away the Transformer's name...not to mention setting him on fire. The guardian of entropy named himself The Fallen.
Basically, The Fallen is "Flaming Robot Judas".