Zelda will ask Link what he wants to do afterwards just before getting on the Demon Train for the last battle. Each response will change the ending sequence.
Complete the Sand Temple, then return to the Sand Sanctuary with the Sand Wand. Raise the sand in the Sanctuary to find three big green Rupees.
Take the small Goron to Castle Town. You will eventually be able to talk to him and he will say he is discouraged by city life. The small Goron has spent all of the money that his grandfather gave him. Select "Cheer up" as a response. The Goron child will get happier. Then, select the first option in the conversation. The young Goron will thank you and give you Goron Amber as a reward.
Keep hitting Zelda the whip or boomerang when she is inhabiting a phantom and she will eventually fight back.
As you collect stamps for Niko throughout the game you can unlock various new (or old) pieces of equipmnet.
While riding in your train in the Ocean Realm, you will sometimes see golden dolphins that swim alongside your train. While they are doing that, bring up the menu screen that displays the "save" button. The dolphins will start doing dances and tricks in front of the train after a few seconds.
Go to the Forest Realm and talk to the person at Rabbitland Rescue. Collect the indicated number of rabbits in the Spirit Tracks to unlock the corresponding item.
When you get the bunny net you can unlock useful items.
After you have completed all of the temples, go back to the Snow Sanctuary and speak to the Lokomo there. He will explain how he wants to decorate, and requests that you deliver him a vase. Go to the Ocean Realm, and buy a vessel from the fortune teller woman on the island. Deliver it to the snow Lokomo. After talking to him, the vessel will be sitting next to him. He will thank you and reward you. However, if you break the vessel with your sword, he will demand that you buy and bring him a new one.
Find the Air Stones at the indicated location to learn the corresponding song that can be played on the Spirit Flute. Tap an Air Stones to hear the song and see the proper colored notes that should be played on the flute. To memorize the song, take out the Spirit Flute and play the song as it is appears. You can then refer to the songs from the Collection menu.
After you get a letter from Niko in Aboda Village, visit him to get a stamp book. Find the fifteen various stamp stations in different areas that you can visit on the rail map to get a stamp. Return to Niko after getting the indicated number of stamps to unlock the corresponding reward.
Search the following locations to find the stamps for Niko.
Complete the indicated Take 'Em All On challenge at the southeast corner of Hyrule Castle Town to unlock the corresponding item.
When you are in the final room of the Tower of Spirits, with the four Phantoms, take control of the Torch Phantom. Before you do anything else, send Link to the Safe Zone on the west side of the room. As the Torch Phantom, go to the door leading to the area where the Warp and Normal Phantoms are located. Light the torches and the door will open. A Phantom Eye will appear next. Enter the area with the Warp and Normal Phantoms. Go to the east side of this area, beside the Normal Phantom, and talk to him. Now that he is out of the way for the moment, switch to Link. When the Phantom Eye cannot see you, and the Warp Phantom is heading to the east side, run in and take control of him. You will now most likely be spotted; run back to the Safe Zone. When the Phantoms stop chasing you, go to the area with the two switches. Because there is sand blocking this area, Zelda cannot go with you. Let the Phantom Eye see you, then run across the sand. Next, warp to the Phantom Eye as Zelda. Step on the switches. The door behind the Normal Phantom will open. Next, take control of the Torch Phantom again. Stand beside the Normal Phantom and talk to him again. Switch to Link, and when the Phantom Eye cannot see you and the Warp Phantom is moving to the east side of the area, run in and stun him. Do the same to the Normal Phantom and run into the Safe Zone. Call Zelda, and push the next door open. You can now get the Compass of Light.