Stronghold

Strongholds (previously unofficially referred to as ruins) are a type of structure that occurs naturally underground, and they contain multiple rooms, corridors, stairs, doors and other aspects, as of the Adventure Update. Strongholds also contain a portal room with an unactivated End Portal, which when activated with twelve Eyes of Ender can be used to travel to The End. There are three of them available per world.

Appearance
Strongholds vary in size (though they can be very large). They are labyrinthine and contain several doors and rooms made mostly of Stone Brick, Mossy Stone Brick, and Cracked Stone Brick. Some treasures found in strongholds include Paper, Books, Coal, Gold Ingots, Iron Ingots, Compasses, Red Apples, Golden Apples, Ender Pearls, Iron Chestplates, Iron Boots, Iron Pickaxes, Iron Helmets, Maps, Iron Swords, Obsidian, and Diamonds.

Strongholds are primarily generated underground, often unexposed to the surface and only visible within caves, possibly even underwater caves. In some seeds they may be connected to a dungeon. The terrain generator is apparently incapable of discriminating between strongholds and standard blocks, as map generation features such as Underground Ravines and Abandoned Mine Shafts cut indiscriminately through strongholds, often making the strongholds difficult to navigate. It is unclear whether this functionality is intended or not. Strongholds are vacant except for regular mobs that spawn under normal conditions. Strongholds are the only location where Silverfish can spawn, created when someone mines one of the blocks within. No new mobs besides this have been added to strongholds as of yet.

The majority of a stronghold is composed of many random hallways, pillars, spiral staircases and regular stairways formed with stone slabs. There are both wooden and iron doors throughout the structure, the iron ones operated by nearby buttons. Since all doors seem to generate facing the same cardinal direction, some are initially open, which can lead to the unusual case of an open iron door which closes briefly when the nearby button is pressed. There are decorative arches built out of iron bars placed along the hallways, and random dead ends at blank walls made of regular stone. Torches and chests are scattered around.

Strongholds also feature various types of main rooms, such as Prison Cells, Libraries, Storage Rooms, and rooms which function as four way intersections with a central fountain or column with torches mounted. There are also unusual rooms with a staircase descending under an arch or bridge against the wall, with another staircase to one side leading up onto this bridge (which rarely allows you to reach anywhere else). While the overall placement and number of these features in the stronghold is random, the features themselves seem to always take the same forms.

Prison cells seem to be generated in pairs in the wall of a hallway and feature iron doors without buttons, and are empty.

The library has two size versions: A small library and a large library. A small library often contains Bookshelves, Wooden Planks, and a chest. The large library contains more Bookshelves, Fences, Wooden Planks, and torches arranged in an upper balcony with a chandelier over the small library, connected by a ladder on the far wall from the entrance. Despite the fixed arrangement of the libraries themselves, the cobwebs seem to be placed randomly within.

Chests can be found on the corner of Bookshelves, and on the upper floor of library rooms. They can also be found on the upper floor of 4-way intersections. Chests in libraries contain paper, books, a compass, and sometimes a map while the intersection chests contain coal, bread, redstone, iron ingots, Iron Swords, Iron Pickaxes, Armor, Ender pearls and Red Apples, sometimes chests can contain a very rare item such as a saddle or a Golden Apple.

Spawning
All Strongholds are located at random in a radius between 640 and 1152 blocks from the origin, 0/0. Due to the generation algorithm, the Stronghold proper may extend further in or out of that circle. The three strongholds are spawned at equal angles from the center point of the world (that is, each stronghold is 120 degrees from the others, measured from the origin.)

Strongholds are still limited to 3 in a world. They can be located using an Eye of Ender.

History
Strongholds were introduced as part of the Beta 1.8 Adventure Update. In early screenshots of Strongholds they were at surface level. This is now extremely rare.

As of the 1.8 Beta, strongholds are vacant except for regular mobs that spawn under normal conditions.

As of Beta 1.9 Pre-release 3, a single or pair of glass towers indicate the location of a Stronghold on top of them, extending from the top of the map to the Stronghold brick. Jeb has stated this is because he forgot to remove the debug towers from Beta 1.9 Pre-release 3. This was fixed in Beta 1.9 Pre-release 4.

In the full release Minecraft 1.0, the End portal room with an unactivated End Portal was added to the Stronghold, and strongholds are still limited to 3 in a world.

Trivia

 * End portals may become useless if there is an Abandoned Mine Shaft or a Ravine cutting through it.
 * Due to the way the overground generates, if a stronghold ends up generating on the surface the area where it passes above the first surface block will be deleted making finding a stronghold that generated like in the first screenshot impossible.
 * There's an extremely rare chance of 2 Strongholds joined together, sometimes even 3.

Bugs

 * Often when a stronghold overlaps with another underground structure torches or iron/wooden doors will generate floating. If it's a iron door, you can fix it by hitting the button next to the door, which will cause a redstone current to be sent to the door, causing the door to do a block update (in this case, opening) which will make it realize that it's floating and it will destroy itself. The same can be done with wood doors, but no button is needed.
 * Often when Torches in Strongholds generate, they emit no light, but the torch itself is bright.
 * Sometimes, generated doors are made open, not closed. (Buttons close the doors temporarily.)