Princess Peach's Castle/Bowser's Domain

A large area supposedly beneath Princess Peach's Castle. Bowser's Domain was discovered by YouTuber Marionova64 and showcased in his videos Breaking the Barrier, Subterranean Terror and The Man Dressed in Green.

Bowser's Domain is a secret hidden base supposedly ruled by Bowser that can be accessed via falling down a second trapdoor in the hall that leads to Bowser in the Dark World, although the second trapdoor can't be accessed in regular copies of Super Mario 64. Bowser's Domain also contains a strange version of the Bowser Room.

Layout
Bowser's Domain presents itself as a large area of the castle accessed via falling down a second trapdoor in the hall that leads to Bowser in the Dark World.

Main Room
After this, Mario will land in a large hexagonal room, right in the center of a carpet similar to the Foyer's. This room has several doors and paintings hung up on the walls, two of these paintings are Bob Omb Battlefield's and Whomp's Fortress', there is, however: a third painting of a Goomba in a green field and a fourth painting of two Pokeys in a desert area, both with a door underneath. There are several other doors, too. Behind the player's landing spot is a large slope with a red-carpet texture and a sign warning to not open the door at the end of the slope (Presumably written by Bowser). The walls next to the slope have a different texture to those in the main room, as they seem to resemble a star night sky similar to that of the painting on the second floor. At the very end of the slope is a door using textures found in both Ocarina of Time and Wet-Dry World.

Bowser's Courtyard
After opening the door, the player will enter a smaller area similar to the Castle Courtyard, with some windows, a large fountain in the center of it, and two more doors with the same texture. However, most notably, a painting using the Wet Dry World skybox can be found directly in front of the fountain, the painting is accessible, although it is unknown where it takes the player to.

The Basement Halls
The door directly in front of the player's landing spot leads to a strange room similar to the entrance of the Basement, with two paintings: Jolly Roger Bay's (JAP version) and Lethal Lava Land. There's also a tunnel-like entrance extremely similar to the Basement. The tunnel leads to an extremely confusing complex of halls, and a sign written by a Koopa worker, documenting their work and complaining about how King Bowser treats his workers.

Koopa Library
Another one leads to the Koopa Library, full of shelves and signs; and weirdly enough, a large dark purple Cap Switch, with a sign warning the workers to not interact with it as it can unlock all Cap Blocks, which is helpful to Mario. There's also a door with a Bowser painting hanging above it, and a sign warning us not to open it, as it leads to the infamous Bowser Room.

Three-Way Room
A mysterious room with three ways, the one infront of the door leads to a crawl place that takes the player to a smaller chamber, it doesn't seem to have a mayor purpose as of yet.

Bowser's 'Greenhouse' and the room of the Man Dressed in Green
As demonstrated in the latest video, there's a strange, garden-like room with several bridges. Most importantly though, there is a mirror similar to that in the infamous Mirror Room. Mario can use an invisible cap hidden inside a small chamber to go through this mirror. Going through the door at the end of the mirror will not take you to the same room you entered through, instead, to a smaller room similar to Bob-Omb Battlefield's, with a painting that displays a front-facing image of Luigi, if Mario goes through this painting, he'll be transported to the main room again, but now, playing as Luigi.

There's two of these Greenhouse-like rooms, the second one has no mirror, is much bigger, and has several bodies of waters, the door at the end of this room leads to a similar hall to the one that takes to the basement of Princess Peach's Castle, much longer, with many other doors, and seemingly infinite, it may be a variation of the Fourth Floor.

Video evidence

 * Video Evidence 1 - Breaking the Barrier
 * Video Evidence 2 - Subterranean Terror
 * Video Evidence 3 - The Man Dressed in Green