Chapter 1:1. The black hole secret in the temple.
Chapter 2:Nothing.
The Interlude:1. Both areas accesssible through hidden passages in the first room.
1.1. The "HI PONTO" room.
2. The area where the "Fireworks" achievement can be unlocked.
2.1. The light bulb hidden in that area.
3. The "Dance in the Sky" room.
Chapter 3:1. All items, rooms shown on the map and quests.
2. All Greek letters.
3. The "Shortcut Genius" Achievement.
4. The "Redundant Bird" area.
5. The "Habanero Apologize" room.
6. Both museums.
7. The Figure Space.
7.1. All empty rooms reachable by going off the rails in Mofa Dabasu.
7.2. The Red Forest.
8. The village beneath the Infinite Darkness.
8.1. The button that opens the mini figure.
8.2. The hidden room under the button.
8.3. Mina (the girl Cilia calls a vomit tail).
8.4. The Mini Figure.
9. The unique dialog triggered by using the debug mode to reach Hannah without opening the door.
10. The naked guy in Megabyte.
11. All additions to the ending. (I had a look at the script to make sure I didn't miss anything.)
12. Lu going insane and teleporting the characters to a special part of the disorder.
13. The hidden passage above the gate guarded by Oldboard.
14. The glitch described at
http://nifflas.lpchip.nl/index.php?topic=6087.0 (performed it at both locations mentioned).
15. Paying Laserdisc with Tova's invisible artifact.
The menu:1. The "Juni and The Puzzle Piece" mini chapter.
1.1. The "Tobias Chilli" room in it.
1.2. The two empty rooms to the left and right of the starting room that can only be reached with the debug mode.
2. The "A Toast" mini chapter.
2.1. The four empty rooms to the left and right of the tower that can probably only be reached with the debug mode.
3. The debug area.
3.1. The three hidden pixel art Knytt.
3.2. The "Because it's tradition" room.
3.2.1. The room with the spiral and the spikey creature in the middle.
4. The "Neon Fall" mini chapter.
4.1. The area containing the "Pew Pew" achievement.
4.1.1. The Tiny Figure.
4.1.2. The alternate path near the beginning of it that allows you to skip part of the main area.
5. The "HUMLab Murder Mystery" mini chapter.
6. The "Sync Transform" mini chapter.
7. The "Comic Sans Challenge".
8. The "Papyrus Challange".
9. The area above the chapter select room.
9.1. The "Anti Figure" mini chapter.
9.2. The room that allows you to transform into a ball.
9.2.1. The area with the "It's complicated" room.
9.2.2. The disco in the menu.
9.3. The "Stranger Dream" mini chapter.
9.3.1. The dead end you reach when trying to leave Utopioca after entering it.
9.3.2. The area with Do where you end up when failing to reach the Disorder exit in time.
9.4. The "RPG" mini chapter.
9.4.1. The area that unlocks the "Heroic Dance" achievement in the PS3 and Vita versions.
9.4.2. The room above the waterfall with a nearly unreachable hidden passage leading to a void screen.
9.4.3. The void screen which can only be reached through a very difficult jump that requires moving upwards, letting go of the wall at the right moment, and jumping right after that.
9.5. The mini chapter similar to "Sync Transform" that's reached by touching the rotating and pulsing square.
9.6. The "Ask The Characters in Knytt Underground" mini chapter.
9.6.1. Dora's challenge.
9.6.2. The secret passage that lets you skip half of it.
9.6.2.1. The second secret passage.
9.6.2.1.1. The hidden room above the "?" room.
9.6.3. All the questions and answers, including those that are answered in mini chapters. (Didn't find any secrets in them.)