Clipping into the geometry is useful for entering the Water Temple without Iron Boots or a Hookshot, which also allows you to complete the Water Temple as a child.
Since the water level is high as a child, you'll need to fall out of bounds to get under the island above the temple entrance.
As an adult, clip into Lakeside Laboratory and swim towards the corner of water, on the west edge of the island. As you swim, the camera will get stuck near where you clipped, but if you swim near the ground, it will focus back on you.
Getting to the fishing pond is used in order to steal the rod in order to activate Reverse Bottle Adventure (RBA).
This method of pond early is really hard to pull off. Link has to be in the perfect position or he won't make it.
The Ruto Letter cannot be obtained by simply touching it. It can only be obtained while in the diving animation.
As a child, you can easily obtain the Golden Scale Early from the Fishing Pond. If running a route that avoids the scale, you can either use Navi Dive if Navi is available, or clip out of bounds from Lakeside Laboratory.
As an Adult, the entrance to Zora's Domain is permanently blocked off by a wall of ice, but the entrance to Zora's Domain still can be reached by clipping into Lakeside Laboratory once the water is raised.
If the water is NOT raised, you can enter Zora's Domain with a Superslide Teleport