How to find: Coming into the tower from Blue Level, walk up the winding stairways clockwise. Pass three corners. In the fourth, look around – you should notice a narrow vertical slit in one wall. It's easy to miss, so if you're worried you might get your count wrong, make sure to look around carefully in every corner as you progress up the stairs.
How to unlock: Any Blue Cube from Blue Level will do, but for what it's worth, there's an extra Blue Cube on the tree in the Blue Tree / Red Tree puzzle room of the Green building set of puzzles. It's up in the higher 'branches' and it looks like it was put there as a wink-wink-nudge-nudge.
How to find: This Black Forcefield is technically in the starting area before Blue Level. At the location where you place the Blue Cube into the recepticle to get into the tower, instead of entering the tower, walk right along the platform, then immediately follow the stairs down the tower. The third flight of stairs should have a Black Forcefield and the fourth flight of stairs a door closed from the inside.
How to unlock: You need a Void Cube to dispel the Black Forcefield, but you really only need the Void Cube temporarily. Follow the stairs inside the newly open area until you reach a blue button; drop the Void Cube and quickly push the button (before the white-out teleports you back to the Void Cube's spawn point).
You can finish Blue Level after you've pushed this button.
There are two Red Cubes in this room and a Yellow Laser. What you need is two Red Cubes and a Yellow Cube. It follows that you need at least one other cube!
Yellow Cube: You can get a Yellow Cube from Yellow Level. You'll need to mostly solve it, since it's on a Yellow Tree that lives in the Yellow building that's the very last set of puzzles in the area, but it has no purpose in Yellow Level (except in activating a White Forcefield you want to deactivate), and so makes for a convenient carry.
You can also take the Yellow God Cube out the same way, but you can't use it for the the Secret Passage route. You can do some very cursed things with two Yellow Cubes in the vicinity, though...
Third Red Cube: There are two Red Cubes on a Red Tree in the Red Room. You used one of them to get to the Red Stairs. You can bring the other one through as well, then turn one of the three Red Cubes into a Yellow Cube with the laser.
(You can also bring in both a Red Cube and a Yellow Cube, which will let you hoist the Yellow Cube up more quickly.)
This puzzle is a bit annoying to solve, so here's a step-by-step guide for you:
Note that this setup is a bit precarious, and if you return to this puzzle, you might find it in a messed-up state. You should be able to fix it quickly by repeatedly doing this sequence of gravity switches (starting on Green): Blue, Green, Orange, Green. In my experience, after at most three times the configuration returns to its intended state.
You can peek past the White Forcefield to get your Blue Cube placement just right, but it depends on the White Forcefield's current configuration. It moves, so you can wait some seconds to see whether a favourable angle will open up.
You can, of course, also just drop it somewhere near the vertical bands of light, then turn off the Forcefield and fine-tune the placement by hand.
How to find: Not all of the pillars in the Green Pillar Canyon behave normally. Let yourself fall and drift to the wall furthest from the door leading to the canonical next section. You should start seeing a platform 'hovering' in 'mid-air'. Let yourself fall toward it to discover the hidden room.
How to solve: Hover over the Large Pinball Puzzle icon this path leads to for guidance.
This puzzle can be really annoying to solve and is impossible for the hard of hearing unless you've gathered screenshots from a different run beforehand, so here's a quick cheatsheet how to solve it:
You want to move five Blue Cubes from Green Level to Blue Room.
If you're having trouble finding them: Take all the Blue Cubes from the Blue River Watermill puzzle – there should be three (two for diverting the Blue River, one for keeping the White Forcefield open that allows the Blue River to flow) and then look down from the platform the source trees are on. There is another Blue Tree there, not needed for Green Level. You can retrieve another two Blue Cubes from there, although you'll need to get into the branches to pluck the top one.
To get the river to flow through the door, you need all five Blue Cubes from the Green Level, plus the Blue Cube you used to open the door leading to Green Level, for a total of six.
Two of these will activate the White Forcefield that allows the Blue River to activate the Blue Watermill in Blue Room, and the other four Blue Cubes are needed to direct the Blue River around the obstacle by diverting it left, right, right, left on the platform with the obstacle (under the Blue Watermill).
When dropping the Orange Cube into Stairway Canyon, pay attention to the cube's shadow. It should fall onto the side of a stairway. (You can recover from this if you hit something else, but it'll make things easier.)
You'll need to drop this cube into the Blue Stairway River Puzzle room, so make sure you know where you're taking the cube. If you've lost your way, park it somewhere and explore the area.
How to find: Blue Stairway River Puzzle room's ceiling has two secret passages in it: One that needs an Orange Cube to open and another that needs a Red Cube to open.
How to solve: Go into Orange Level and find the Orange Tree there. Take the Orange Cube from it, and make your way back to this room. You'll need to be slightly careful, since part of the route involves walking edge-on on the stairways of Stairway Canyon, but it's more forgiving than it looks. The route should be fairly straight-forward once you know you need to take it.
How to find: Blue Stairway River Puzzle room's ceiling has two secret passages in it: One that needs an Orange Cube to open and another that needs a Red Cube to open.
How to solve: You'll need to solve the Orange Cube route first. Hover over the path a bit further up to see details.
Once you've solved Orange Cube route, you have the necessary access to Red Room that you need to solve Red Cube route. For more guidance with Red Cube route, hover over the path leading out to the right.
How to find: Blue Stairway River Puzzle room's ceiling has two secret passages in it: One that needs an Orange Cube to open and another that needs a Red Cube to open. You'll need to solve the Orange route first, since that unlocks the necessary access to Red Room, but once you have that, you can access this route here.
How to solve: Take any Red Cube from Red Room. The route from Red Room into this room and up the ceiling should be fairly straightforward – Pipes Room, for example, comes with excellent stairways to guide you. You'll only need to do some hoisting shenanigans briefly, but you won't even need extra Cubes to do it.
How to find: Not all of the pillars in the Purple Pillar Canyon behave normally. Let yourself fall and drift to the wall furthest from the door leading from the canonical previous section. You should start seeing some pipe-like shapes. Let yourself fall toward them to discover the hidden area.
This is not needed for the secret passage run, but exists to mock you relentlessly – on the secret passage run, you can only access this side of the Large Pinball Puzzle after you have solved that puzzle successfully already.