Note sure if it's been mentioned, but Castle Whiterock was an amazing megadungeon for 3.5E, and it also had a VERY in-depth series of "sub-quests" that provided extra XP rewards, magic item rewards if you went back to the person who gave you the quest, or increased power to some of the named magic items when you did certain things.
Basically, it had Milestones, Quests, and so on, and it wasn't even
4E yet!
I think the setup of the dungeon itself takes a lot of cues from what you guys have been talking about, too: a living dungeon with reorganization, random encounters are not a big deal and mostly there just to drain resources, and key locations that are tied to Quests and other historical info.
Worth looking at, as I've been reading it and the
4E-ness of it jumped out immediately.
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