If you stand next to a Rupee and sidehop over it, you can collect the Rupee without seeing the text that normally pops up
Collecting a Rupee while in the air or on Epona will also skip any Rupee text
Link has different animations depending on whether you go through the left or right door at a set of double doors. The right door animation is faster than the left by about 20 frames, so it's generally better to go through double doors from the right side. This does not apply to doors that go into a loading zone.
(Note: On Wii, this is reversed due to the entire game being mirrored. So opening left doors is preferred on Wii)
When you press Z to call Midna for a Midna Jump, there's an animation of her flying towards the target spot. For certain jumps, there is 1 frame where you can input a jump before the animation starts and skip needing to watch it. This is used primarily in Castle Sewers.
Besides Lantern, you can also burn webs using the Ball & Chain, and shooting Bomb Arrows at them
If you C-Up before calling Midna, it will skip the mini cutscene of the camera panning and allow you to transform immediately
You can sidehop through the steam jets on Death Mountain without needing boots on. You require a shield to do this though
When standing still, if you hold L for 2 frames before rolling, you will get to max speed faster than just rolling from standstill
Using C-Up followed by an aim item immediately afterwards lets you aim faster than any other method.
When you're stuck onto walls with Double Clawshots, you can get into first person aim quicker by pressing the clawshots button, then tapping L quickly.
Normally when you walk near some gold bugs, they will fly away, but if you hold L and walk towards them they won't be scared off.
If you resurface from underwater quickly and then try to sink again, the air meter will appear quicker than it normally does. This is usually a bad thing, as having a quick air meter can make tricks like Pillar Clip or the Morpheel backup impossible.
There's a few places that will automatically set the time of day to a certain time when you savewarp there. For example, savewarping in Palace of Twilight will change time to night. Savewarping in City in the Sky will set time to Noon.