One of the things I think is very important for the creation of a good megadungeon is a solid background for its existence. By that I most certainly don't mean pages upon pages of details about the dungeon's construction and all the little events that took place in and around it. That strikes me as largely useless. I do, however, find utility in a "framing device" that gives some context to the whole thing -- something to provide a rough explanation for what's going on in the dungeon, even if it does obey its ecological and physical laws quite distinct from those of the world outside.
So, in thinking about it, I'm going to go back to the same well from which I drew "The Ruined Monastery" in issue #1 of Fight On! In that adventure, I created an order of Lawful monks dedicated to St. Gaxyg the Gray, who built their monastery on top of an ancient site suffused with the power of Chaos. The monastery thus served to "bottle up" Chaos, keeping it locked away in its subterranean stronghold and eventually, it was hoped, driving it out completely. Unfortunately, the monks grew corrupt and fell victim to greed both within their community and without, which led to the downfall of the monastery about a generation ago. Without the monks there to maintain the wards against Chaos and manning the battlements against its onslaught beneath the surface of the world, evil is growing and expanding once more.
That's the basic explanation of the megadungeon itself, which I plan to use to justify all the oddities within it. As I currently see it, there will be some surface ruins (of the monastery itself), as well as a couple of sub-levels that form the "topmost" levels of the dungeon. Beneath them, behind slowly-unraveling wards are the levels of the dungeon proper. They're a mix of natural caves and hewn rooms, the latter being part of the monks' centuries-old war against Chaos. Consequently, there are some "waypoints" and "bunkers" scattered throughout the lower levels, which in times past were used by the monks in their crusade. Some of them can still provide delvers with temporary "safe zones," but many, if not most, have been overtaken by Chaos and have been turned toward evil purposes. And, of course, as one gets deeper, the power of Chaos grows in strength, especially as one reaches levels that even the monks never entered, for it's here that the sources of the megadungeon's evil are to be found.
How's that sound?