7. Phantom Ganon
Although his name is a bit confusing (He's not exactly Phantom 'Ganon' more of a Phantom 'Ganondorf', but that's not as fun to say) he is definitely one memorable boss.
The boss battle itself is incredibly fun. The atmosphere is perfect and everything fits with the recurring theme of the temple, paintings. Unlike the Poe Sisters, he actually goes back into the paintings! It's all about illusions in this battle.
Even in the beginning of the battle you're like 'Oh no! It's Ganondorf!' and then he takes off his face! O.O It was all an illusion.
The design is interesting despite looking almost exactly like Ganondorf his skull face gives it a different kind of flare.
It bothers me a tad that you have the same strategy of battling him as you do later in the game when battling Ganondorf, just repetitive gameplay, but it probably has some meaning.
The entire battle with Phantom Ganon is basically foreshadowing of your later battle with Ganondorf. This Phantom Ganon is like the sum of all fears for Link and the embodiment is of the only thing that Link remembers about Ganondorf. The only time that Link had seen Ganondorf prior to his actual battle with Ganondorf, he was seen on a horse.
The little details and overall affect of this boss makes it stand out from other bosses who may have had similar concepts.