Pit Stop (But Don't Stay Too Long), easily one of the most somber tracks in the game, which is appropriate, since they are used for the Town of Restless Spirits, Moorcroft Manor, and Emberlight, the town of Gremlin Outcasts.
As awesome as the normal Clockwork themes are, none of them can top Around the Clock Workshop, which is used for the Deconstruction Zones, and is easily the best track in the game and really gives you vibes that you are in Gremlin territory.
Throughout the game, you'll regularily hear the Main Theme, a remixed version of Cradle, which is a glorious theme that plays in the RJP, the IMF, the Concrete Jungle and the Dark City. There are also other remixes of the Main Theme. Crash Course, a toned down version of the Main Theme, plays during the starting sequence. On the other side of the spectrum, Shadow's Swarm is an excellent Dark Reprise that plays when you are fighting the Swarm. As one commenter puts it, "When you hear this theme, it's not because you're about to complete your mission. It's because you're struggling against an entity that is barely understandable by the Spiral Order. An entity that was not meant to be.", and A Good Knight's Rest is an utterly beautiful track that plays in The Sanctuary, a safe haven from the Swarm's grasp.