Stone Tower
Go ahead, jump on the three blocks, then step on the switch, which moves one of the blocks. Play the Elegy of Emptiness to create a clone which will keep the switch activated, then throw your Hookshot at a target to the west. Put on your Stone Mask to stay invisible for Cyclops Statues, then step on the switch, turn into Goron Link (or Zora Link) and play the Elegy of Emptiness to create another clone. Wear the Stone Mask again, then throw the Hookshot higher to the east. Step on the switch, which moves the third block, turn into Zora Link (or Goron Link) and play the Elegy of Emptiness. Next, take off your mask and jump on the three blocks to cross southward.
3DS: Use the Hookshot westward and leave the switch for the time being.
N64: Step on the three switches on the other side to switch back blocks to their original state, then use the Hookshot on the left, step on the switch and play the Elegy of Emptiness.
Throw the Hookshot higher towards south (stand near the last pillar), step on the switch and play the Elegy of Emptiness.
3DS: Next, drop back to the previous platform, step on the switch as Goron/Zora Link and play the song. Then use your Hookshot to go back up.
Now throw the Hookshot toward northeast. Stand on the switch as Zora/Goron Link and play the Elegy of Emptiness again. Reach the north part of the tower thanks to the three blocks.
N64: Step on all three switches to move the blocks again.
Then use your Hookshot to the east. If you got the Scarecrow's Song, you can get on this pillar, play the song and use your Hookshot on the scarecrow to get hearts, rupees and ammos in pots. Throw your Hookshot to the south and there again you can play the Scarecrow's Song. Then use the Hookshot towards southwest and switch on the Owl Statue!
Now you can see three switches. Step on the right one (according to the map), play the Elegy of Emptiness, then play it on the left one, and finally play it on the middle one so all three blocks form a path. You can put a fairy in an empty bottle by breaking pots behind you, then jump on the three blocks to get in the... owl.