Guess I'll chime in with some of my favorite songs, since it seems to be what the cool kids are doing.
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First, I have to go with my favorite Final Fantasy of them all, Final Fantasy VI, and mention Dancing Mad - the four part final boss theme which introduces you to a new section of the piece each time a part of the boss is conquered (see the original SNES version for the best method of melding the piece together - the GBA version screws it up royally.) Ultimately, after beating the 3rd tier of the boss, the organ strikes up that familiar opening theme, Kefka descends, and the theme really picks up. If you last long enough (or force Kefka to last long enough), the familiar sound of Kefka's laugh completes the track prior to the loop. Beautifully composed throughout the battle, this is one of the SNES's best tracks.
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Second, switching gears to my second favorite video game series, the Tales series, I have to go with "Fighting of the Spirit" from Tales of Symphonia. Anytime Sheena attempts to forge a pact with any of the world's Summon Spirits, she (and the remainder of the party) are forced to fight the Spirit as part of the test. The theme used for the battle is quick, catchy, and really drives the complexity of the battles.
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Third, I must make mention to Zelda's red-headed stepchild of the series, Zelda II, and bring up the beautiful Palace theme. However, I feel this song really was brought out in Super Smash Bros. Melee on the Temple stage. A great song that set the tone for the complicated fights deep in the Temples.
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Fourth, while I've seen a few mentions of Mega Man 2, I'm going to take it to his next adventure, Mega Man 3, and bring up Snake Man's theme song. While many Mega Man songs can get mentioned, I may feel a special attachment to Snake Man, as this was the first stage I ever played in a Mega Man game, and instantly fell in love with the music of this series. (On a side note, Snake Man's theme, along with Guts Man and Heat Man themes, were remixed in Mega Man 7 for the Robot Museum stage
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Finally, my fifth pick has to go to a new favorite of mine, Xenoblade Chronicles, with its boss theme "One Who Gets In Our Way". Oftentimes played for bosses (such as the Metal Face Mechon), this theme is a great blend of rock and classical type musics to spur you on as you continue on those battles of the game. Monado, lend us your power!!
(Ok I lied, I have to include Rainbow Road from Mario Kart 64. Just too awesome!!)
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