Master glitch
First, ride Epona to Gerudo Valley. Cross the bridge and go to the carpenters' tent. While still on Epona angle to the right and try to go in the right side of the tent. When you are lined up like this, press A to speed up and hold left. If you did it correctly you should be inside the tent without Epona. This will get easier after you get the hang of it. There are many things you can do with this glitch (too many to list here.) The best way to find what you can do with it is to explore on your own. All you need to know is that you will automatically be on Epona whenever you enter an area where Epona was programmed to go. Here are some glitches the master glitch leads to:
Invisibility
Getting Stuck Above Lake Hylia
Riding on Epona While Being Dead
Getting Under a Minute in the Marathon Race

Invisibility
After doing the master glitch warp to Lake Hylia and you will be invisible. Also, if you can do swordless Link you can be invisible anywhere you ride Epona. To do so, use Farore's Wind on Epona, warp to a temple, go inside, and use Farore's Wind to return to the warp point.

Get Stuck WAY Above Lake Hylia
First, go to Lake Hylia and go into the Water Temple. Play Farore's Wind. Now go to the carpenters' tent and do the master glitch. While in the tent, warp to the Fire Temple. Then go in the temple. Play Farore's Wind and warp back to the point in the Water Temple. When you exit the dungeon you will be on Epona WAY above the lake. You cannot get down so you must reset the game.

Ride on Epona While Being Dead
Lose almost all your life. Make it so that one bomb hit will kill you. Do the master glitch. Warp to outside the Fire Temple, go see the Gorons, and then exit through the Lost Woods. Then go Kokori Forest. Go to the bridge where the running man finishes. Throw a bomb and exit at the same time you get hit. This may take many tries. You should be taken to Hyrule Field and be on Epona without any life if it worked correctly. You will not be able to use any weapons even with the swordless Link glitch. Link will die whenever he gets off Epona.

Get under a minute in the marathon race
First do the master glitch. Then ask to race the running man. You should already be on Epona when you leave the tent so you will gain a couple of seconds. If you use this with the swordless Link glitch you can finish in under a minute (and still lose). At the end of the race still going full speed use the Ocarina to get off Epona. These two glitches will help improve your time.

More glitches coming soon.....