Echo Tune- This tune is taught to Link by Nayru. Once Link gets the Harp of Ages from Nayru's House, a message comes with the Harp teaching Link the tune. The Echo Tune awakens sleeping portals. You can see the differen't spots where there are portals on your screen. Play the tune and they will turn to portals along Link to pass through time.
Currents Tune- This tune is taught by a man just outside of Symmetry Village in the past. After exiting the village from the left exit. Head left, and up two sets of stairs. At the top-right of the screen Link can dive under water. Go through the side scrolling area to find a man. Play the Tune of Echos and he will teach you the Tune of Currents. This tune allows Link to travel from the Past to the Present from any location.
Tune of Time- Once Link learns this tune there is no reason ever to use either of the other tunes. Link learns this tune from Nayru once Link saves her in the Past and they come back to the Present. When Link plays this tune he can travel from any point in the past to the present, or from the present to the past.