The Fire Stone, Water Stone, Thunder Stone, and Leaf Stone are all found at the Sea Cottage when showing Bill's grandfather a Growlithe/Vulpix, Staryu, Pichu, and Oddish respectively. There is also a 0.20% chance to receive one from Mystery Gift, being the only repeatable method for them.
A Moon Stone can be found at Tohjo Falls, and another will be bought by the player's mom when saving up $15000. There is also a Clefairy event at Mt. Moon where, if triggered between Monday night at 8:00 pm and Tuesday morning at 4:00 am, a breakable rock will be produced with a Moon Stone. Wild Clefairy also have a 2% chance to be holding one.
The Sun Stone is the first prize in the Bug-Catching Contest.
Evolution Stone - Bulbapedia
