The name comes from the Transformers Generation 1 villain introduced in the animated movie, which was the first time the character had been adapted for a new television series. Each series in the Unicron Trilogy dealt with the classic Transformers lore of the war between the Autobots and Decepticons, modified for a modern audience. It began with the introduction of the Mini-cons, smaller Transformers (less than human-sized) that can combine with the larger robots to give them powerful upgrades. The story of their origin and the war to claim their power leads into the introduction of Unicron himself. Energon and Cybertron continued after Unicron's initial defeat with additional problems that arise that could lead to the destruction of Cybertron.
Cybertron the toy line (and thus the gimmicks and preliminary story) was developed by Hasbro to be a continuation of Armada and Energon, but when the anime, Transformers: Galaxy Force, was developed it was made as a different continuity line altogether (direct references are made between Armada and Energon, while Cybertron is a little bit more vague about it). The English dub of Cybertron gave it stronger ties as per Hasbro's intention. After some time of contradictory statements, Cybertron was eventually retconned by the Japanese fiction itself.
Because Armada is what kicked off the trilogy some people refer to it synonymously with that series.