I'm in the spitballing stage of setting up the same sort of thing, for an open-table campaign sometime in the next year or so.
My megadungeon is going to be dug into the face of a chalk cliff - like the White Cliffs of Dover.
The dungeon itself is going to be an elaboration of Petra and the West Wycombe Caves. There will be two main ways in - the more obvious way, from the main entrance in the cliff face and the more hidden ways into the face, and down into the complex from the top of the cliff, above.
The dungeon's levels, in terms of general power of the monsters and such, will be easiest near the face of the cliff, becoming more difficult as the adventurers move inward. The rationale for this is that there have been adventurers coming here for many years, clearing the galleries that are easiest to reach, and retiring or dying before penetrating too far. The more powerful monsters tend to push the weaker towards the entrance, as a buffer against annoying treasure-seekers.
There will be jungle at the top of the cliff, running back to a mountain range. There will be entrances into the deeper levels of the complex hidden in this jungle - perhaps the jungle hides the remnants of the civilization that started building the complex. The jungle is going to be really, really nasty. I'm thinking forgotten temples completely overgrown by the vegetation, a Lost World vibe with dinosaurs and giant apes and lizardmen/snake-people. Still - if you want to venture into the jungle, or have some way of flying over it (without being eaten by pterosaurs, etc), you can reach the hidden entrances to the more remote galleries.
Within the complex, most of it will be excavated from chalk and flint. The lower ranges of the complex extend below sea level, and are mostly, but not entirely, flooded - it would appear the water table has risen since the construction of the complex. Air circulates through the complex through tens thousands of minuscule cracks, holes, natural chimneys- near the cliff face one can often smell the sea, and near the surface there are the root systems of the colossal jungle trees.
There will be areas of natural caves interspersed with worked areas, and many of the worked areas will be expansions of natural caves. One will be able, with time and experience, to have a general idea of how deep beneath the surface one is by a sense of the humidity of the air, the style of the stonework and so on.
I'm thinking that near the cliff face, the structure will mostly be organized as a series of galleries - this is where the builders built inward from the cliff face, in stages. There will be many entrances, but mostly inaccessible - you have to climb out along the cliff face, and there are a few nasty creatures that live out there (hang-gliding hobgoblins?), as well as the physical problems of reaching the more remote entrances on a cliff face of eroded chalk. The structure here will be mostly homogenous - one building style, for the first two levels or so in from the face.
After that, there will be sections, vertically organized, leading down from the upper works near the jungle surface. Given the easily workable nature of the chalk strata, it was almost easier to dig down than build up. So there will be identifiable areas which are connect to other bits, but they'll have their own individual idiosyncracies.
Most of these 'silos' will be connected to each other by natural caverns, but over the centuries, individual organizations have come and gone, controlling a number of areas and enhancing their connections, or fortifying their space against the depredations of their neighbors, building invasion tunnels and collapsing them, which leads to each of the individual silos being connected to many others, by more and less difficult/obvious ways.
I'm thinking that the campaign will probably start from the main entrance, and they'll work out ways of travelling deeper and deeper into the complex. When people want out, they'll have to decide whether they can retrace the path to the cliff face, or, if they're lost and turned around, whether it's best to simply head upwards to get out. Of course, then they'll be in the jungle, which brings its own set of problems.
The base of operations, at least in the beginning, will be across a channel (think Calais, across from the dungeon entrance at Dover). The adventurers may eventually set something up on the other side - until then, 'home base' is a day's travel over the ocean, while the forward base will be rather more precarious - a camp on the shore, protecting their boat.
Anyway, that's what I have so far.