From the Nightprowler RPG (an all-thief game, with character classes like burglar, swindler, assassin, spy, etc.), the best medieval fantasy prison ever:
Ad Silencae
When people are sent "at Silence", they know to abandon hope, for there are none left for them.
Ad Silencae is a massive, large tower, with no doors or windows, save its entrance gate. The inside of the prison is a black, dark pit, with cells piled all-around, on several stories.
Catwalks, rejoined by bridges line the walls between the cells and the pit.
Only some meager torchs illuminate the place.
Security has always been the first and foremost concern, trumping everything else. Nothing has really been made for evacuating wastes, for example. They just slide through the pit through the cell's portcullis. The odor is unbearable for all but the most hardened jailers. For prisoners too, but their comfort really don't matter.
On the bottom of the large room, the wastes slide and fall in an actual pit in the center. The pit is deep enough for human falling to break their bones. A series of grate block the way to the sewers (which are inhabited by various hostile creatures, from monstrous centipedes to ratmen to some fiends).
Jailers patrol constantly the catwalks and bridges, with crossbows. Because of the darkness, a lighting device has been designed and mounted on their crossbows. It consist in a little bullseye oil lantern with mirrors, and a lense that concentrate the light into a ray. It also helps in targetting. The constant shuffling of these crossbow light rays is eerie and unerving.
The name of the prison comes from its first rule -- prisoners aren't allowed to speak. Not the smallest sound. Failure to comply lead to getting one's tongue cut off, and his lips stitched together. If the guards don't identify who spoke, everyone in the cell got his tongue cut off. The poor bloke with stitched lips may only poor a little part of the noxious soup prisoners are fed, and become quickly starving.
This don't prevent people from talking, but only faint whispers when the jailers are far.
Prisoners are frequently moved from cell to cell. They don't stay more than 3 days in the same cell. This is to prevent prisoners from organizing themselves.
When a prisoner is switched to another cell, all prisoners in the cell are made to put their back against the wall. Each one is aimed by a jailer, all having a ray of light in an eye. One is told to move forward. The portcullis is lift up just enough for him to crawl under. The portcullis is then lowered. If any of the other prisoner move, bolts are fired. The same process is used to make the prisoner enter his new cell.
Some stitched lips are not genuine, but are spies. Some prisoners, before being send to the pit, cut a deal for a reduced length of penalty in exchange for informations. Under the guise of changing him of cell, he is led to a room where his thread are cut, and he'll tell everything he's learned. Then, his lips are stitched again, and he's sent to a new cell.
Finally, each prisoner that enter in the prison get a number on his left shoulder, marked with hot steel. When his term is finished, the number is "blanked" with another hot steel marking, that leaves a solid rectangle mark. People who have been sent to As Silencae several times -- and survived it -- have several such burned out rectangle on their shoulder and chest. Any person caught outside of the prison with a number marked on his shoulder through hot steel is killed on sight. Theoretically, as noone ever escaped Ad Silencae.
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