In Majora's Mask, all Great Fairy Fountains exist on the same map. This means that clipping out of bounds in the Great Fairy Fountain can allow for fast travel between the various areas of the overworld. In Majora's Mask 3D, this is done through the use of Goron Missile. The order of the fountains can be seen in the image below.

To jump a single fountain away, simply line up on the flat ground of the fairy fountain and Goron Missile in the direction of the fountain you want to jump to.
To jump two fountains away, the setup is slightly different depending on if you're jumping east or west. See the setups below for each one.
To jump three fountains away, line up as shown in the video below.