Bongo Bongo is one of my favorite bosses in all Zelda games. Very unique and inspired many future Zelda bosses, it always appeared to me he was the spirit of a man who was tortured to death, the music was awesome with him singing, he was defiantly a challenge at first, and he is the largest boss in the game.
Twinrova is the most interesting, and I'm gonna tell you why.
Twinrova is an interesting boss in that there are two of them. Now, there are other bosses in the Zelda series of which there are two or more such as Molodorm in LttP, but Twinrova is unique in being two different bosses, with two different attacks, fire and ice. These are also not just two visually different attacks, but their effects are also different.
In the first stage, it is very interesting how Kotake and Koume's weaknesses are each other's powers, and the gameplay involving use of the mirror shield to deflect the beams at the other was fun and challenging.
Then, of course, they combined into one boss, and the gameplay became even more fun, now using the mirror shield to absorb attacks, and having it reflect as well.
Another part of what made defeating Kotake and Koume so exciting was that they had long been setting up obstacles, and had first used the Iron Knuckle to keep you at bay to kidnap Nabooru, then had used her as a minion. So, it was an emotional victory of sorts to defeat them, after having dealt with so many of their minions.