After reading through the comments in the Grognardia post on an ideal megadungeon format, I discovered that many people were covering some of the same ideas I presented. I should have read those comments first, so that I could point out that that list of special "hub" rooms (what some people call "Saturday Night Specials") would fit the role of "modular megadungeons", as expressed by Ed Dove in particular. Each region equals one module; there are multiple regions (modules) in each level, but they are designed to fit together conceptually, perhaps answering Zak's objection to the modular approach. Furthermore, there could be free-floating modules with a monster theme but no "hub", or only a very minor hub, which could be dropped into any level at any location.
The physical arrangement of modules (regions) within a level is completely up to the GM; each GM's implementation of the megadungeon is unique.
And you know that list of hub concepts for the level? Which probably has a unique monster or two listed next to each concept? That list of unique monsters -- basically, the bosses -- can be annotated to show relationships. The lich-king may be subservient to the undead priest; an ogre boss in one region may be unaware of the goblin-king, but the goblin-king's minions may be stealing small quantities of gold and provisions from the ogre, and the ogre may be looking for someone to blame.
The concept list would also include any special magic items, cursed items, or otherwise notable items. Think of this as a four-column table, with Name, Concept, Monster(s) and Item(s) as the table headings. If we're talking about a series of commercial products, each module for a level would include the entire level list, plus the most important monster/item from each of the other proposed levels, so that the GM has a central place to look up important items and drop hints or directions to important beings and objects.
Since the rooms that aren't "Saturday Night Specials" are all pretty generic (three to five types per region,) you need some way to distinguish them. The encounter list for each region can begin with a descriptor word, perhaps randomly selected, which is combined with the actual room type to create a specific key phrase the GM can elaborate on during play. "Filthy storeroom" and "Manure-filled storeroom" will seem like very different places.