Ben's theme "Dharmacide", "Life and Death", and "Locke'd Out Again". Michael Giacchino earned his Emmy award for this show.
One of Losts most famous usages of non-original music was "Make Your Own Kind of Music" in the season 2 première, in which Desmond plays it in the hatch during the opening scene. Not only it caused a crazy Soundtrack Dissonance, but had lyrics which still define the characteristics of the character introduced to this day.
The opening of season 2, after we see Desmond in the hatch going about a normal life. After an explosion interrupts him, he uses a series of mirrors to look further and further through the complex. His gaze continues up a shaft to the faces of none other than our heroes throughout the first season, on the island.
Season 3, "Tricia Tanaka Is Dead:" Hurley and Charlie are trying to jumpstart a van by rolling it down a hill and popping the clutch. Just as they are about to crash into some big rocks, the engine fires up, and the car's tape deck starts playing "Shambala"
John Locke's second theme, which appears often during his flashbacks, is a fantastic, emotional piece that accurately portrays how far he's come.
The music from "Exodus" is stunning, especially over the saying goodbye montage in the episode.
Similarly Ben's theme, known as "Dharmacide" is almost perfect in representing Ben. There's the sinister first part, the tragic second part and a sort of mixing together for the thrid. Pure bliss. Also the S5 Ben centric version is even better
"Hollywood and Vines", aka the "setting off" theme as it always plays when a group is going off to explore the jungle and has an air of adventure and mystery about it.
The haunting "Ocean's Apart", which plays at the end of "Stranger in a Strange Land," and is the only good thing about the episode. It serves as Juliet's character theme. Especially in The Incident when they combine the "Ocean's Apart" theme with the frantic strings and the "Life and Death" theme while Juliet is being pulled down into the Swan. Hauntingly poignant.
The theme introduced in the episode "Across the Sea" that serves as a theme for the light at the heart of the island. While some may debate whether or not the light was properly executed as the mysterious source of everything, the music sure as hell sells this aspect perfectly, inspiring the right balance of awe and apprehension.
The medley of themes from the final scene of the show as the various characters meet up in the afterlife and Jack dies peacefully on the island is a guaranteed tearjerker. 'Moving On'. You will be bawling by the seven minute mark.
The theme that frequently plays when important characters die or during other emotional moment is "Life and Death." Used when Jack resuscitates Charlie, when Shannon learns about Boone's death, when the passengers get onboard Flight 815 in the flashback in "Exodus, Part 2," when Charlie dies, when Sun brings Ji-Yeon to Jin's grave, when Juliet dies, when Sun and Jin dies, and when Jack 'remembers' his life on the island, among other moments.