1.

Link the game with Oracle of Ages after completing both for the true final boss.

2.

Winter snow lets you walk over water — use it to reach otherwise inaccessible areas.

3.

Autumn seeds from Gale Trees reveal hidden paths in Holodrum.

4.

The Master Sword is only obtainable in a linked game (both games completed).

5.

Trade secrets between linked games to unlock unique items in each.