One element that I think is lacking in the mega-dungeon campaigns I know of is the party's interaction with reoccurring and looming villains antagonists. That's an element that really adds enjoyment to the wider scope campaigns I've been in, but you don't hear much about it in the big dungeons. Blackmoor probably was best at it. In Greyhawk you don't hear much about it, other than Obmi being referred to as a reoccurring villain. And I don't know the specifics of that. I'm have a few ideas I might try to work into my dungeon. Any thoughts?
Besides the obvious Fraz and Iuz appearances I'd say that Zagyg's indifference is the big enemy for Castle Greyhaek. The big end dungeons that I've ran have kind of of that indifference over pure rottenness but I think it, GH castle, was influential to me in its ruined nature mostly because lack of information didn't provide any other influence. Usually I've had pure evil locales on a smaller scale with a few exceptions. I've always been big on recurring bastiches and I think the unifying similarity of them all is that they're everywhere.
I think I might put an orc king in there, and work on making the Bloody Head orcs an ongoing threat on the lower levels.
The cult of Nerull/the Scarlet Brotherhood are a big presence in my dungeon, but I haven't put much thought into any of the NPCs to make them more than just another encounter. The head cleric makes a good candidate.
And then there's the big kahuna wizard that lives on the 11th level. He may have to throw out some tendrils to announce his presence before the PCs get there. Some servants, apprentices/henchmen or something.