My last campaign involved a mega-dungeon, depending on how you define "mega," I suppose. It had 11 levels with about 15-20 areas per level. Different factions controlled various levels. It culminated in a final showdown on another plane with a shadow dragon. (I wanted this campaign to involve a dungeon and a dragon.)
The basic premise was that the dungeon was the manifestation of the dragon's power while it was trapped in another realm known as The Shade. Once a week or so, the dungeon (called "The Delve" by the locals) would appear in a cursed forest known as The Duskwood for about 24 hours. Signs and portents in the nearby town of Grimdark would point to its arrival at which point adventurers could plumb its depths. I put a timer on it: In 20 weeks, the Shadow Wyrm would escape and wreak havoc upon the land. In the meantime, the presence of the dungeon had corrupted the forest, once home to the reclusive fey.
I set it up as a town-to-dungeon D&D experience with consistent phases of play: Warm-Up Phase, Town Phase, Travel Phase, and Delve Phase. There was also a Short Rest/Camp Phase when the PCs rested. Rests were reconfigured to 8 hours for a short rest and a week for a long rest. Since the Delve only appeared for somewhere around 24 hours at a time, the players had to manage their travel time and number of rests they took per expedition. There was a hard-stop in real time around 4 hours into the session at which point the Thrice-Damned Horn would sound. If the PCs didn't beat feet out of the dungeon at that point, they risked being trapped when the Delve re-entered the Shade. (This meant your character was driven insane and became an NPC.)
To me, it was enjoyable because of the number of meaningful decisions that were built into the structure of the game. The players could figure stuff out and strategize to achieve the goals they themselves set week to week. As DM, it was easy to run because of the consistent structure and the set adventure location. This meant prep was a little heavier, but it was fun to put together.
@Lanliss and @Valmarius both played in this game, so they may have some other thoughts.
This is a pretty cool campaign idea, thanks for sharing it.
I need to add more time elements to my own games... doors that open for only short periods of time, or shrines that grant a boon only on a night of the new moon. If you manage campaign time carefully enough, there is a world of opportunity here.