Easy Money
Outside Clocktown in the Termina field head toward the Milk Road. Near the trees you will be attacked by a vulture who is ready to steal your Rupees, and other items. If you are able to beat the vulture you will be rewarded with 200 Rupees. You can deposit the money in the bank and then go fight the vulture again. There is no limit to how many times you can fight the vulture.
Fix The Signs
First cut up a sign then play the "Song of Healing" which is C-Left, C-Right, and C-Down. The sign will fix itself. (aka Zelda's Lullaby)
Jump Forward 12 Hours
Play this song with the Ocarina to travel forward in time 12 hours: C-Right, C-Right, A, A, C-Down, C-Down
Slow Down Time
If you play the Song of Time backwards, time on the clock will move slower, but you will still move at the normal speed. This is very useful when running long distances or when trying to prolong game time.
The song is: C-Down, A, C-Right, C-Down, A, C-Right.
To return the normal flow of time, simply play the song again.
Stone Mask Secret
A hidden feature of the Stone Mask is that it will camouflage Link. This is helpful because most of the enemies will not be able to see you. Bosses will still be able to see you, but most of the typical "run-of-the-mill" bad guys will ignore you.