The Reconfiguration Matrix (or internal reconfiguration matrix) is a device incorporated into Optimus Prime which allows him to transform his body into numerous entirely distinct robot and vehicle modes.
The first mention of the Matrix was in the packaging bio for Prime's Go-Bot incarnation, though later information indicates that it was also a part of his "Laser Rod" form as well. The mechanism by which the Matrix operates is not known, but it seems certain that it has some kind of advanced matter-energy manipulation capabilities, as it not only allows Prime himself to assume dramatically different physical forms, it can reconfigure the bodies of others, and even produce new bodies for disassociated Sparks.
Prime used the Matrix to generate a new form for Ironhide after he was badly damaged at the battle of Moon Base Four. (From last year's shitty sorta half-decent Botcon) An even more noteworthy event involving the Matrix was the return of Ultra Magnus from his death at the hands of the Decepticons. Since Magnus had briefly carried the Matrix of Leadership, his Spark retained its consciousness of the world outside the Allspark. Learning that Galvatron II had gained command of the Warworld, he contacted Prime through the Matrix of Leadership, and used the Reconfiguration Matrix to resurrect himself. Interestingly, Magnus' new body also has the ability to transform itself into many physically disparate forms, but whether this means he also carries a copy of the Reconfiguration Matrix is unknown.
Note: The Reconfiguration Matrix should not be confused with the Matrix of Leadership, an unrelated device also generally associated with Optimus Prime.