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Chapter II: "Disaster"
- Switchworks' "Nocturnal Type". It's nothing but fast-paced, catchy techno, and also happens to be the song used in the tutorial for the game.
- "Entrance" by Ice. The two challenging and borderline eerie hidden songs on its splash screen are part of a single song called "Precipitation at the Entrance". The devs even had "Entrance" remixed for their other rhythm game, Deemo.
Chapter III: "Cytus"
Chapter IV: "The Silence"
Chapter VI: "The Lost"
- While it's not particularly challenging to play, Selfish Gene is quite pleasant to listen to.
- Bloody Purity, a beautiful and catchy piano track, is easily the best theme in Chapter VI. It begins rather slow, but the speed ramps up to near-insane levels towards the end.
- "The Blocks We Loved" is the shortest song of the chapter, but it's also one of the more memorable ones for being a remix of Tetris's "Korobeiniki".
Chapter VII: "Loom"
- "The Last Illusion" easily stands out as one of the game's grandest instrumental songs.
- "L" by Ice, which is known for being That One Level even on Easy, being the only song with an Easy chart rated level 9. The violin and the shameless employment of drag notes makes you feel like you're ice skating with your fingers.
- "L2", accessed by holding down the "L" logo until it changes color:
- The first act (red "L" logo) is somber and heavy on the violin and piano, with a difficult section full of trills at the end.
- The second act (blue "L" logo) continues where the first act left off, and turns into an intense trance track that pushes players to their limits. Its Hard chart is not only one of the hardest in the game, but also has the most notes of any chart (before Chapter L came along), surpassing longer songs like "STORIA" and even the seven-minute-long "Vanessa"!
Chapter VIII: "Another Me"
- "Axion" stands out for being both very difficult yet ridiculously catchy, with fast-paced and futuristic-sounding beats causing a real treat.
- "Q" might be repetitive, but with your ears constantly bombarded with awesome by the song's Epic Riff, it simply doesn't get boring.
- "Reverence, a relaxing and beautiful drum 'n bass song that serves as the last song in the chapter.
Chapter IX: "Buried"
- Out of all the Vocaloid songs in the game, "COMA", the second-to-the-last song from Chapter IX: " Buried" is the most notable; it's by far the only song in the game to have Tagalog lyrics, unlike the Japanese or Gratuitous English lyrics of the other Vocaloid songs.note .
- "Codename: Zero". Notorious for being That One Level with a painfully fast tempo and multiple "killer" patterns, but all the hell perfectly fits a truly fast-paced and heavy electronic song.
Chapter X: "The New World"
Chapter K: "Knight"
Chapter K is a Concept Album, telling the tale of two childhood friends who become separated and meet years later, with tragic results.
- "Knight of Firmament" (AKA "The Chevalier") is a remix of "Holy Knight" and is about Iris resolving to use her sword to change everything back to the way it was.
- "Lord of Crimson Rose" (AKA "The Queen") is generally thought to be rated far too highly in terms of difficulty. However, this doesn't matter when you're listening to this great rock song that seems to represent Rosabel's Superpowered Evil Side emerging after her corruption from the evil grimoire.
- "Predawn" (AKA "Farewell"), which probably represents Iris preparing for the fight against Rosabel.
- "The Fallen Bloom" (AKA "The Duel"), which represents the climactic fight between Rosabel and Iris. Notably, both vocalists are the same ones for "Knight of Firmament" and "Lord of Crimson Rose", and it features a short cutscene depicting Iris finishing off her friend by stabbing her through the chest, which permanently replaces the song's image in the menu once you play it.
- "Where You Are Not" (AKA "Curtain Fall") is a beautiful and epic-sounding track whose sad melody represents Iris's feelings after being forced to kill her friend Rosabel.
- "Music.The Eternity of Us" (AKA "Alternative") can evoke a wide variety of feelings: on its own, it sounds like it represents a Heartwarming Moment in the chapter's story, but when put in the context of the plot, the second title seems to indicate that it's actually an Alternate Universe where the conflict never happened and the two girls stayed friends. This stark contrast with the previous songs turns it into a huge Tear Jerker.
Chapter R: "Retro"
As indicated by the title, all of the featured songs in Chapter R are chiptunes, with their respective eyecatches rendered in beautiful pixel art.
- "Let's Go on an Adventure" by 3R2, a bouncy, happy-go-lucky tune with a cheerful blue-haired girl skipping down a path lined with rainbow-colored macaroons in the background. In short, Sweet Dreams Fuel incarnate.
- The final song of the chapter, "conflict (YM2151 Edit)", a chiptune arrange of the infamous BMS song "conflict". ...which appears in the chapter as well as the chapter's sole non-chiptune song and Secret Level.
Chapter M: "Million"
As a thank-you to the playerbase for reaching the 1 million download mark, Rayark produced a special "Million" chapter consisting of arranges and medleys of past Cytus songs. And it's free for everyone who already owns the game.
- Area184 -Platinum Mix-, which takes the original "Area184", adds a dose of awesome, and also borrows from Persona's three "Eyes" songs for good measure.
- "STORIA" by xi and Sakuzyo, a medley of "Halcyon", "Niflheimr", "VitMaster" (as a non-chiptune arrange!), "Black Lair", and "AXION". A four-minute Rhythm Game equivalent of a Boss Rush.
- "Gardenia" takes "Hard Landing" and "Logical Steps" to create a relaxing song that would be right at home playing during the credits.