1. First, the opening where it shows the story is as follows in the japanese version :
SEVERAL YEARS AFTER GANNON WAS DESTROYED,LINK LEARNS FROM IMPA ABOUT THE ANOTH- ER SLEEPING PRINCESS ZELDA. HE IS TOLD SHE CAN ONLY AWAKEN WITH THE No.3 TRY- FORCE SEALED IN THE GREAT SANCTUARY AT DISVALLEY. TO REMOVE THE SEAL, CRYSTALS MUST BE EMBEDDED INTO A STONE STATUE STANDING IN 6 SANCTUARIS. LINK SETS OUT ON AN ADVENTUROUS QUEST...
While the american version says :
AFTER GANON WAS DESTROYED, IMPA TOLD LINK A SLEEPING SPELL WAS CAST ON PRINCESS ZELDA. SHE WILL WAKE ONLY WITH THE POWER OF NO.3 TRIFORCE SEALED IN A PALACE IN HYRULE. TO BREAK THE SEAL,CRYSTALS MUST BE PLACED IN STATUES IN 6 WELL GUARDED PALACES. LINK SET OUT ON HIS MOST ADVENTURESOME QUEST YET...

2. North Castle is less detailed in japanese version, while the american version contains the pillars, torches, purple curtains, and the longer hallway.

3. Link has a slightly different color palette, the brown is somewhat darker in the japanese version.

4. The enemies are completely differnt. In japanese version, they are just like colored baloons with eyes. Fairies are red, strong enemies are blue, weak enemies are white(screenshots coming soon).

5. The battle music is completely different as well (hopefully will be available soon).

6. Raising your levels is a little different. In the japanese version you can choose any level you want to raise when you earn enough points, while the US version has requirements for each.

7. The game pauses during loading (hence it being on a disk). It will say "W A I T" before you go into towns, dungeons, etc.

8. The water (ocean) in japanese overworld is animated.

9. The six temples are colored white, while the US vesion has numerous colors.

10. Most to all sound effects are different.