Essences can be found at the indicated locations.

Leaf Essence: Tree stumps, your houses, and Torajiro's house.
Fire Essence: Cool Trees and Roy's furniture store.
Heart Essence: Lovely Trees and phone booths.
Water Essence: Fountains.
Diamond Essence: Kayaking race course in the Mangrove Forest.
Star Essence: Lamp posts and Lovely House 2.
Brown Diamond Essence: Flowers and the Town Hall.
Bubble Essence: The Curio Shops and the snowman from the Synth-O-Matic.
Moon Essence: Dr. F's Laboratory and the Heliport.
Question Mark Essence: Garbage cans and the Gondola Summit.
Planet Essence: The ski slope, stone pillar, and slide.