I suggest my players do not read the mega-dungeon threads!
What is a mega-dungeon?
It is not, as I've seen said on certain places on the interwebs, a monster zoo or fun house. It is certainly possible to construct one that way, but any such thing reserves the title of dungeon, not mega-dungeon. Would you seriously have 300 rooms and fill 100 of them with a single type of humanoid? Or worse, each room having a different humanoid? A good mega-dungeon is not that.
So what is a mega-dungeon? Besides awesome?
The answer is complex.
At it's most basic, it's a structured environment for play. It has advantages in that it provides a simple understandable setup for focusing on the most enjoyable part of play (collections of interesting choices). It limits player choice from "I can do anything" to an acceptable number of options.
It has other advantages in that it allows players to set their own rate of advancement and risk and reward because of it's open and non-linear nature.
It is a dynamic environment, one that is constantly changing and growing as the players affect it. They are impossible to be cleared.
It is more akin to a city in modern RPG's like shadowrun or vampire then a traditional dungeon. A living breathing environment that allows the players to enact their will and exert their agency in a structured way.
It is a mythic environment, with strange portals and interesting happenings, not just a warehouse of corridors.
What are the key features to allow this to happen?
Multiple entrances, no less than 1 entrance for every 30 rooms, preferably more.
Various entities, factions, and power structures that exist, each with their own agendas. This includes special areas and other reasons to return to earlier levels.
A totally non-linear design, allowing the players to direct their choices and choose their fate.