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Starbuck's piano version of All Along the Watchtower from season 4 was a literal jaw-dropper. Not only is the song awesome on its own terms, but the way the song was played in that episode answered at least two of the season's biggest mysteries at the same moment.
Season 4's Diaspora Oratorio, which played as the fleet arrived at the first Earth. It's played completely straight, which just makes the reveal of Earth as a wasteland that much more heartwrenching. McCreary considers it his best work on BSG.
Zarek was one of the few main characters not to have received his own motif, so when it came, it was pretty damn good. His character inevitably went to his death an hour later.
"Metamorphosis One" by Phillip Glass, which was featured in an early scene in the series, where Starbuck and Helo are sitting in Starbuck's apartment on post-nuclear-holocaust Caprica. The version in the linked video doesn't even begin to convey the atmosphere this piece creates in the actual episode. Original footage of that scene is also available on Youtube, albeit at much lower quality.
Neither is the final piece of music in the series. All Along the Watchtower - played by Hendrix.
Bear's three classical piano pieces "Battlestar Sonatica", "Elegy", and "Dreilide Thrace Sonata No. 1" are the most beautiful pieces composed for piano to be put on a soundtrack album. "Battlestar Sonatica" is an elegant tribute to Beethoven's Moonlight Sonata. "Elegy" is intended to sound as if it is being played on a wrecked old piano in a bar, and transcends the limitations of the instrument. Finally, "Dreilide Thrace Sonata No. 1" is the reason pianos were invented. It is absolutely lovely to hear, being written for a grand concert piano, is a masterpiece in terms of the complexity of the composition and sound, and is easily the most emotional of the three piano pieces, especially in the final minute and a half.
Of course, music by Richard Gibbs in the Miniseries is pretty sweet. "Are You Alive?" is wonderfully creepy.