Up until the Summer 2012 Update, both free to play and premium players were able to earn them (through quests), however only premium players were able to spend them at various EP stores. After the Summer Update, these old EP were converted to coin at a ratio of 1:10.
Everyone now starts the game with 100 EP (for accounts created after the update) and 500 if your account predated the update. Empire Points serve to unlock premium content, such as Booster Packs or Premium Civilizations, and Vanity gear, thus allowing the game to become truly Free to Play.
Empire Points are earned through some major quests, through levelling up and from participating in the Alliance Wars, only available to level 40 players.
Empire Points can also be purchased via Steam micro-transaction or with Microsoft Points.