Rubies are vendor currency used to purchase game items to advance your city or army faster than waiting out the required cool down periods for building, training, travelling or (resource) production periods. Items that can be purchased include (but not limited to) Fortuna's Chance tickets, resources, nanos to aid production, Chronos (speed up boosts), armour, completion grants, ceasefire treaties, mass nullifiers, dragon eggs. Items are purchased using the Shop button in the lower control console.
All new accounts start off with 10 rubies and cannot be earned in normal game play. Rubies can only be purchased through PayPal or by credit/debit card, or through completing online surveys. Occasionally, Kabam opens contests or give-aways with prizes that normally consist of rubies.
Update: As per an official communication from Dragons of Atlantis to all players, rubies are being replaced with Facebook Credits. This is because Facebook policies require all such premium currency to be in facebook Credits. The change is being rolled out to a some players, and will be extended to everyone soon.
Google+ users still use rubies as currency, which can be bought through Google Checkout.