From Galaxypedia

Starbases include player made Starbases (Starbase), Planets such as Frion I, Aqueous II, and Myriad III, and NPC Starbases such as the Derelict Station, Mothership, and the Freedom Base.

Most Starbases come with defenses that include either Turrets in the case of the Mothership Starbase or Fighters in the case of Myriad III (although they are only available for the faction after a Level 3 upgrade). Two of these Starbases don't come with defenses, these being Freedom Base and Derelict Station, but instead have a boost to the usual spawn rate and amount of Ores floating around these quest Starbases.

Overall, Starbases are a primary source of defense, Fighter-filled firepower, and great places to plan out another counter attack or strategic retreat. The main strength and weaknesses of Starbases include several factors such as defenses, player count, and Starbase level; basically, plan right, or your entire faction will hit oblivion inexplicably quickly.

Some other lore or quest-based structures appear similar to regular Starbases, but do not share the same functions (such as docking, spawning ships, or assimilation). The Remains of U.N.E Starbase 12 is one such structure.