These are used to buy goodies in the ancient coin shop. You can get ancient coins by running the labyrinth.
You can use ancient coins to buy the following items:
1) Malicious Bug Charm - 1,200 (only once a week)
2) Lv 22-60 Accessory Chest - 40 (Spend it here early game for % main stats for rings and necklaces)
3) Lesser Ring Charm - 40
4) Greater Ring Charm - 120
5) Lesser Necklace Charm - 40
6) Greater Necklace Charm - 120