The title "Prime" isn't given any special meaning in the first two seasons of the cartoon show -- in fact, it isn't really seen as a title or a rank either, just part of Optimus Prime's name. To modern fans, the rank "Prime" is one of the single most important concepts in all of the Transformers brand, being the designation given to the leaders of the Autobots and the bearers of the highly powerful artifact, Autobot Matrix of Leadership. However in this series, only two Primes are ever named (Optimus Prime and his successor Rodimus Prime), and the term isn't given an actual definition. Alpha Trion and Ultra Magnus are both Autobots who have possessed the Matrix, yet neither of them are ever called Primes.
Nevertheless, a succession of previous Autobot leaders do appear in the season 3 episode Transformers: Five Faces of Darkness: Part 4 (#3.4), during Rodimus Prime's spiritual trip inside the Matrix. None of these are given names, and it was only in 2010 that the Transformers: Animated tie-in book The AllSpark Almanac II retroactively assigned individual names to each, merging them together with various different characters in an effort to "clean up" the messy early history of Transformers fiction. In a chronological order, they are:
* Primon, AKA the Alpha Prime -- the first documented bearer of the Matrix, he is the first ancient leader Rodimus meets during his journey. Actually the merging of two, originally distinct but similar characters: the unnamed Matrix-bearer from the cartoon (called "Ancient Robot" in the episode script) and Alpha Prime from one of the later comics. In a curious development, later Prime "lists" disregard this character, for as-of-yet unexplained reasons.
* Prima, the "first Transformer". In subsequent media, he is the leader of the original Thirteen (the first Transformers created by the god Primus), but in this show, he is an ancient gladiator who unsuccessfully rebels against his Quintesson creators. In the script, his name is simply "Powerful Robot", and before the release of The AllSpark Almanac II, he was regarded as a separate character from the Prima introduced in the comics.
* Prime Nova, who led a successful rebellion against the Quintessons, driving them off the planet. Called "Brooding Robot" in the episode script.
* Guardian Prime, the first actual Autobot. He was killed by evil warrior robots belonging to the then-formed Decepticon faction. In a somewhat questionable stylistic choice, his visual appearance is almost identical to Rodimus Prime's, and due to an animation error, he initially appears as Prime Nova. The episode script gave him the name "Pre-Transformer".
* Zeta Prime. Simply called "New Narrator" in the script, this character only leads the Autobots for a very short time.
* Sentinel Prime, Optimus Prime's direct predecessor, whose history reaches way back to the era of Prima, during which time he was called Sentinel Major. After the death of Zeta Prime, he took over as the Autobot leader, earning the name Sentinel Prime. Under his rule, the Autobots developed and mastered the art of transforming, and successfully defeated the Decepticons. After the so-called Golden Age of Cybertron, the Decepticons returned, being able to transform themselves, and their leader Megatron killed Sentinel. Alpha Trion kept the Matrix of Leadership safe, waiting for the arise of a new Autobot leader. Optimus Prime was then constructed by Alpha Trion himself from the dead body of Orion Pax. In the episode script, Sentinel Prime is given the name "U-Haul Robot".