Elphaba is the 'real' name of the Wicked Witch of the West in Wicked. Elphie is a nickname she is given within the musical.
Athena is after the Greek goddess; when I first saw her she just 'said' "Hi I'm Athena get me out of here!"
Helios/Selene are Greek gods too, well Titans. Of the Sun and Moon respectively.
Rivergrace is a name of a 'pretend' flower in a Nintendo mini game. It just has a beautiful flow to it, making it perfect for the right rabbit. We named Morningstar to go with her (adopted together) and then realised it's a name given to both Jesus and the Devil. Given Morning's scrappy demeanor, it's appropriate.
Persephone, another Greek goddess. Morpheus, a Greek god, the god of dreams as he looks like a dream.
Arce arrived with bridge bunny Iris. Iris is the Greek goddess of the rainbow and Arce is the goddess of the Double Rainbow.
Erasmus is a Greek name. He was advertised as special needs due to being a biter. His name means "worthy of being loved" because he is. Oh, and he hasn't bitten once, but he IS deaf. And still worthy of being loved.
Yuki is Japanese for Frost. His middle/rescue name is Winter. Niji, we picked out before we met him. He was to be bonded with Arce, and Niji is Japanese for Rainbow.