There are many iterations of Autobot City in the Multiverse. Most can be considered NPC facilities, however. There are currently two that are considered important "in play" at present.
The first is Autobot City proper, which is located on the Earth that corresponds with Transformers-1. It is a massive, Transformer-sized city-fortress, capable of withstanding considerable bombardment and even a full-scale attack. It serves as Autobot headquarters on that planet, and is supplemented by the wreckage of the Ark, which served as Autobot headquarters until the construction of Autobot City. It is an important Union holding and can often be used as a command-and-control nexus in the region in an emergency should another facility be unavailable.
The second is Metroplex. Metroplex is an NPC Transformer that is a mobile, living chunk of Autobot City proper. More information can be found on his page.