As for these achievements I would not say much as you collect them simply by doing the main story:

The 3 main puzzles are:

1. Lever 1: up
   
2. Lever 2: down
   
3. switch 12 o'clock
   
4. press right square

This one is missable.

Don't complete the jukebox puzzle.
For this achievement you have to do it "the other way round".
While fixing the jukebox, place the cogs at the right side as it is displayed at the image.
With this placement, the direction of the cogs is counter clockwise and any track played is reversed.

So If you press 5F on the jukebox buttons, this achievement will unlock.

There are 2 Instruments located at mother's wing:

1. the music room you find the harp
   
2. the music room you find the piano

Simply just interact with them and the achievement unlocks.



Again 2 things you have to interact with, located at the brother's wing:

1. the robot in the play room
   
2. the slot car racing trac when you are in the sleeping room

There are 3 phones to find. Just interact with them and try to seek help:

1. Father's Wing in the garage
   
2. Father's Wing in the room with the jukebox
   
3. Brother's Wing in the room with the pool table

They are pretty obvious to find, because you "see" them, as they are making sound.
Approach and activate them:

1. Father's wing: Garage
   
2. Mother's wing: if you are in the corridor heading to the music room, the radio is through the door at the oposite site
   
3. before you see the dude in the cage at the top of the stairs
   
4. after yo freed the dude, simply follow him and he leads you to the radio at the kitchen (?)
   
5. you used 3 cogs to enter, you can "see" it already

There are 12 gems in this game:

Father's Wing (2)

1. At the garage.
   When you enter take the door to your right and look at the toolbox on the left table.
   
2. In the library.
   When you enter go straight to the shelf and remove the books from the second rack (counted from the bottom). Behind a book is the gem.

Mother's Wing (2)

1. In the walk-in closet
   Enter the closet and turn left.
   
2. At the garden area.
   At the right side of the tree

Brother's Wing (2)

1. At the playroom
   At the floor is an air plane besides a robot. Near the airplane
   
2. At the pool table room
   At the table with the cards

Bob Area (5)

1. Aftear you reach the attic (the top of the dark stairs)
   At the same side as the wind chimes. Left from the wind chimes at a balk.
   
2. after you freed the locked up dude, follow him and he leads you to a grandfather clock you'll see a high cupboard. Open it and look at the cups at the first rack (right side)
   
3. In the same area
   Search the chimney, look at the chimey, do a 180° turn and look at the table
   
4. In the same area
   there is a dining room, look at the long table
   
5. In the same area
   on the kitchen table, there is a gem inside a box

Outside (1)

1. When the lobby is caved in,
   leave the lobby and go outside (left) into the garden, look behind the second bench of the left side

Now you can enter your way to the control room.
As you walk along the long hallway the echoes of the memories inside the gems will be repeated.

After the lobby is caved in, you can enter "outside" into a garden area. Simply follow this path and keep walking till you see a path between two lampposts. Follow this one and while you are looping back, this achievement should pop.

The final area in the house.
After the floor in the lobby has caved in, do any other (non-story-related) achievement before you try this.
Hop down the stairs and you will encouter the monster.
As you proceed at some time many stuff (like bottles) are over the floor. Pick that up and throw these things towards the monster. After 10 times the achievement should be unlocked.