"One Winged Angel" is arguably the most popular Final Fantasy final boss theme because it represents the series' most popular villain: Sephiroth.
But Destructoid's SWE3tMadness believes that Final Fantasy VI's 'Dancing Mad' can give "One Winged Angel" a run for it's money.

In a very interesting and well-written article, SWE3tMadness explains why he believes "Dacing Mad" is the 'most well-constructed, complex, and thought-provoking boss theme in videogame history.'

Go to the source for the full article - It's worth reading.

I was always bugged by the fact that Kefka seemed to be the only villain in Final Fantasy history that did not have a memorable final speech to make after the heroes defeated him. He just fades away and the tower collapses around him. Then I realized, that I was looking at his fight in the wrong way. His entire boss theme is his last speech, outlining his rise to power, and lamenting his eventual defeat. In order to break it down and illustrate what I mean, I’ll separate the piece into its four distinct movements.

Dancing Mad is the most well-constructed, complex, and thought-provoking boss theme in videogame history. Not based on the song as a whole, but on the details and progression of the piece through the battle. It perfectly represents the villain you fight, as well as the journey through the game to come to that point. Other epically-orchestrated themes may have the advantage of better sound quality as technology progressed, but the strength of this song relies not on the clarity of sound, but how that sound is manipulated and constructed to build a piece that stands on its own as a work of art.

Miss Razz via destructoid.com »