Spiritual Stones & Medallions

Kokiri's Emerald — Defeat Queen Gohma inside the Great Deku Tree.
Goron's Ruby — Defeat King Dodongo in Dodongo's Cavern; Darunia gives you the stone outside.
Zora's Sapphire — Defeat Barinade inside Jabu-Jabu; Princess Ruto hands over the stone (as an engagement gift).
Light Medallion — Given by Rauru in the Chamber of Sages immediately after you draw the Master Sword.
Forest Medallion — Defeat Phantom Ganon in the Forest Temple.
Fire Medallion — Defeat Volvagia in the Fire Temple.
Water Medallion — Defeat Morpha in the Water Temple.
Shadow Medallion — Defeat Bongo Bongo in the Shadow Temple.
Spirit Medallion — Defeat Twinrova in the Spirit Temple.