Video Explanation: http://www.youtube.com/watch?v=-kdZxuCgJ_A
Video Addendum (for Non-Speedrunners): http://www.youtube.com/watch?v=BNzoGjRhA44

In West Clock Town there is a well-known "hidden owl" which can be hovered to. If you hit the Hidden Owl and haven't hit any other owls, when you Song of Soaring there are no points on the map to soar to. You can't choose anything and it defaults to Great Bay, so you can only warp there.

However, what was recently discovered (01/16/14, courtesy Indextic) was that the default point that is selected is actually influenced by the map on your pause menu. It changes depending on the last point you hovered your cursor over on that map. Each point on the Song of Soaring map corresponds to a specific location on your pause menu map.

The glitch saves a few minutes off the Any% speedrun, and is already used in all major speedrun categories. If you'd like to use this in a casual playthrough, please understand you'll have to learn two major speedrun tricks first: ISG and Hovering. Most people can learn ISG in a few minutes, however hovering to the Hidden Owl can be tricky and will take some practice.


Pause Map Point -> SoS Map Point

0) Great Bay -> Great Bay Coast
1) Zora Hall -> Zora Cape
2) Romani Ranch -> Snowhead
3) Deku Palace -> Mountain Village
4) Woodfall -> Clock Town
5) Clock Town -> Milk Road
6) Snowhead -> Woodfall
7) Ikana Graveyard -> Southern Swamp
8) Ikana Canyon -> Ikana Canyon
9) Goron Village -> Stone Tower


Notes:
- The final map point, Stone Tower, corresponds to the entrance of your current dungeon. So trying to warp there while you're outside a dungeon will just get you stuck and force you to reset (aka a softlock). 
- Entering a new area resets the map cursor back to Great Bay.
- Game version and region make no difference.
- Using the control stick while the SoS map is on screen will crash the game.