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.