Most cities have a Saucer Stone Shop. Breeders can get discs here. In some games, they must be purchased with golds, while in others you simply have to match up symbols to win one.
In Monster Rancher EVO, you can tell which shop is the saucer stone shop by looking for the picture of a Disk on the sign.
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Saucer Stone Shop in MR1
Saucer Stone shop in Colno