"We must be miles under the school."
     -- Hermione Granger

Atlas of Hogwarts: The Chambers of the Philosopher's Stone

Located deep underneath Hogwarts, this series of chambers and passages was used to conceal the Philosopher's Stone (a.k.a. the Sorcerer's Stone) and protect it from would-be thieves. Dumbledore placed the Stone there in August of 1991. Then McGonagall, Sprout, Snape, and Quirrell added various protections. To top it off, Hagrid provided a giant, vicious, three-headed dog to guard the trap door entrance on the third floor.
NOTE: The names given to the various rooms are not from the books and cannot be considered canon. They are given here and used occasionally elsewhere in the Lexicon as a matter of convenience. 

Third Floor Trap Door chamber
This chamber is actually the third floor corridor on the right hand side, which has a trap door in the middle of it. Hagrid "lent" Fluffy, a gigantic three-headed dog, to Dumbledore to place in this chamber. The trap door opens to a very long drop.

Devil's Snare chamber
At the end of the long drop through the trap door is a large growth of devil's snare, placed there by Professor Sprout. The devil's snare plant provides a soft but dangerous landing for interlopers. The walls of this chamber are damp.

Passageway
The walls drip water, while the corridor itself slants downward.

Chamber of the Keys
This chamber is a brilliantly lit chamber with a ceiling arching high above. It's full of small, jewel-bright winged keys, fluttering and swirling all around the room. On the opposite side of the chamber is a heavy wooden door. One of the winged keys opens the door on the far side. There are a number of brooms in the chamber. Someone hoping to pass through the chamber must fly on a broom into the air and catch the correct key: a large silver key with bright blue wings.

Enchanted Chess Board
The next chamber is very dark, but lights come on as you walk into it. It contains a huge chessboard. The chessmen are carved from stone and very tall. In order to pass through the room, a person must take the place of a chess piece and successfully play to win. The game is Wizard's Chess, which means that there is very real danger to any human chess pieces.

Troll Chamber
This room contains a very large, very disgusting mountain troll. The smell alone is enough to stop a person in their tracks.

Chamber of the Seven Potions
In this room is found a table with seven differently shaped bottles standing on it in a line. When a person enters the room, magical fire appears, blocking both doors. The fire blocking the door just entered is purple, while the flames blocking the way forward are black.

The potions are a logic puzzle. On a roll of paper next to the potions is this riddle:

Danger lies before you, while safety lies behind,
Two of us will help you, which ever you would find,
One among us seven will let you move ahead,
Another will transport the drinker back instead,
Two among our number hold only nettle wine,
Three of us are killers, waiting bidden in line.
Choose, unless you wish to stay here forevermore,
To help you in your choice, we give you these clues four:
First, however slyly the poison tries to hide
You will always find some on nettle wine's left side;
Second, different are those who stand at either end,
But if you would move onward, neither is your friend;
Third, as you see clearly, all are different size,
Neither dwarf nor giant holds death in their insides;
Fourth, the second left and the second on the right
Are twins once you taste them, though different at first sight.

The solution is this: The potion in the smallest bottle will get a person through the black flame and on to the Chamber of the Stone. The potion in the rounded bottle at the right end of the line will provide safe passage back through the purple flames. 

The Chamber of the Stone
The only feature of this chamber is the Mirror of Erised, within which Dumbledore hid the Stone:

"It was one of my more brilliant ideas, and between you and me, that's saying something. You see, only one who wanted to find the Stone--find it, but not use it--would be able to get it, otherwise they'd just see themselves making gold or drinking Elixir of Life. My brain surprises even me sometimes..." (Albus Dumbledore)