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.