On some screens in the game (in particular the screen before the shadow links in 3-3 as well as the screen before the shadow links in 6-1) JP has pots that are invisible. You can still hit them with your sword and hear a sound, but they do not have any collision.
The old man in the beginning of 2-2 gives you a moon orb when you talk to him after you "feel the strange sensation" on the screen above. However in JP you are only required to talk to him once, while in other versions you are required to be in at least two different conversations before you obtain the moon orb.
The slingshot has one extra textbox in the JP version.
After receiving a particular big gem for the first time in a level, you will receive a text box describing that certain gem under some conditions. In all versions you will get the text if you obtain the gem through a chest.
The difference between the JP version and others is getting the text through the gem cutscene (i.e. getting the gem without hold an item or link). In the JP version you only receive text if green is the one holding up the gem. In all other versions you will receive the text with all color link.
In the JP version if other links that are not selected are in a "busy" state (falling, jumping, etc.) you can switch to them while they are doing their action. This makes things such as gap skips and jump storage much easier on the JP version.
Similar to the Pegasus Boots skip in the same level, you can skip to several screens using the same method in JP.
On the non-JP version getting zombie storage from stairs is not possible.