Thought it might help to compile everyone's answers into one big post. I take no credit for the creation of the below list, this was a creation of everyone here!
Level 1: Sanctuary
1. Smash the clay pot inside the temple when you get your Cube
2. South along the river, on an island.
3. Plat hole left of Baltazar (2nd playthrough)
Level 2: The Forest
1. At the north end of the forest where you fight the sleeping hedgehogs
2. Plat hole on the right side just before the first Eliatrope Path (2nd playthrough)
3. Where you open the door by absorbing energy from the 2 poles. fly to the right
Mystery - In Chibi's temple just before the end of the level
Level 3: The Meadow
1. On an island south in the river, during the meteor storm
2. Plat hole to the right of Grougaloragran dragon after blooming Mina (2nd playthrough)
3. Plat hole in the north side of the river, during the meteor storm (2nd playthrough)
Mystery - Behind Grougaloragran dragon. Grab it after the cut scene
Level 4: The Crater
2. after of the hole (goddess tear 3) if you continue, will pass some prespic running and you should continue until see two way and you must to the right of the screen and to the final you will find other goddess tear
3. Plat hole on the left side of the long path with shooting plants (2nd playthrough)
Mystery - Its in the same room as mount Iznit? model, bottom corner near exit and i think it best to get it befire inspecting the model.
Level 5: The Temple
1. Plat hole to the left of the tree boss (2nd playthrough)
2. To the left right above this one
3. Before enter the great temple, to finish the level
Level 6: Vili Valley
1. Door to the right after some fight, in second scene, just break some crates
2. In a big room where you have to absorv energy from the 2 poles, the left stair has a child and the right one has this, same room you save zora
3. Plat hole in the mystery room (2nd playthrough)
Mystery - South exit of 2nd kitchen area
this mystery is near the hole for the number 3
Level 7: Pliyi di Bili
1. start at the southwest side of the beach, hug the beachline toward the east. The tear will be on the end of the peninsula. It is next to the ledge with a magnolia chalice.
2.continue to hug the coastline toward the east (right), use the dragon to explore offshore again and you will encounter another rock outcropping with the goddess tear on it
3. Plat hole on the north side of the beach (2nd playthrough) – bring a wakfu gel to activate the flame
Mystery – far south west corner, use the dragon to float across the water southward until you find a rock outcrop with a teleporter pad on it. Follow the button sequence to teleport to a higher ledge with the mystery. There will be a telescope and a statue on the same platform.
Level 8: Club Platypus
1. Go down from the start and teleport along the path. It's at the end.
2. After exposing the Shamipus, go to the right and teleport behind the waterfall
3. After exposing the Shamipus, go towards the child and then south. Use the platypus on the hole to go and pick it up from the volcano floor.
Level 9: Pow Wow
1. Inside a plat hole in the first area (on the way up in the left corner after some slapingtrees)
2. On the ledge after the helping the mole
3. In a plat hole just past the ledge in #2
Mystery – in the room with the rings that you need to cancel out to clear a path to the woman that sacrifices herself
Level 10: Rizi
1. Go down from the start
2. Plat hole on the northwest corner of the first area, next to the second Magnolia flower
3. Plat hole on the north side of the cave
Level 11: Mount Zinit
1. In a crate just ouside the stairwell room
2. In a plat hole guarded by lots of little creatures
3. On the north side of a big fight on the mountain
Level 12: Wakanu
1. in the same room as the second !! before the first puzzle in a crate, near the door to the puzzle!! they are left to a purple smoking thing in the floor!!
2. Plat hole left of the room before the 1st puzzle
3. Northwest corner of 2nd puzzle room
Mystery - 2nd puzzle room with the cranes
Level 13: The Islands
1. At the very start of the level, just to the left of the fish oracle in the blue mist.
Level 14: Intiwakana
1. On the far left during the 2nd rock troll fight
2. After the oracle, at the north end of the next arena battle
3. After fighting the giant robot, on the far right. Teleport to a small cliff.
Mystery - after the 2nd rock troll fight, in the room with the fish oracle.