In issues 44 and 48 of Nintendo Power, there are a number of early screenshots from a pre-release copy of Link's Awakening.
These show that the Wind Marimba was originally a pair of cymbals, you could carry more than one of Crazy Tracy's medicine, and you could also carry the Guardian's Acorn. There also appears to be another item that wasn't in the final game that looks like a stone fragment. This was also a prize available in the crane mini-game.

There is also an early version of the world map that is completely different from the final game. It appears to be a highly condensed version of Hyrule from A Link to the Past map. This was likely used as a placeholder during development.
It also seems that the boss battle with Moldorm would have taken place in a room that is completely different from the final version of the game.