From Zelda Wiki, the Zelda encyclopedia
Shadow dungeons often have "scary" or "creepy" enemies, and are usually very dark in atmosphere. They are commonly located in graveyards or very dark places. True to their theme, shadow dungeons are usually populated by demonic or undead enemies, such as Poes, Redeads, and Stalfos, and often contain copious numbers of pits and deadly traps. Puzzle-wise, these dungeons frequently defy the human eyes, often featuring invisible elements or illusions; light may also be required to open new paths, as seen in The Wind Waker with the Earth Temple. Poisonous or toxic elements like fog and certain enemies are present, and are able to void Link's ability to attack temporarily. Many of these dungeons serve as bases of operation for the villains, such as the Black Tower in Oracle of Ages and the Palace of Twilight in Twilight Princess. In the majority of the cases, shadow dungeons are found late in the games.
List of Shadow Dungeons
Infiltrating Hyrule Castle - the fourth dungeon in Four Swords Adventures.