Raguna was kidnapped by the Sech Empire because he was an Earthmate. They took his memories away and planted him near Kardia. Near the end of RF1 he is told his memories will never come back and they don't.
RF2:
Spoiler:
I'm not sure if it was ever explained clearly how Kyle lost his memories. But he does get all of his memories back at the start of the second generation.
RF3:
Spoiler:
Micah was working as a guard in some town and was chasing down some monsters. It was a trap to catch him and the dragon Aquatis (I don't know how to spell his name >.>) takes his memories away. In each of the main dungeons Micah gets a Memory Orb which gives him some of his memories back. In the end after he defeats Aquatis he is told that he can only get all his memories back if he is returned to where he came from. Micah refuses so he only has a few of his memories.
RToD:
Aden and Sonja don't have amnesia.
RF4:
Spoiler:
Lest/Frey falls out an airship and hits his/her head. At the end of the first arc he/she remembers everything, I think. I can't remember for sure if the end of the first arc is the point where he/she gets his/her memory back.
