One of the least-used special abilities of dwarves is their 75% chance to determine new construction. When you read back over the history of the early Castle Greyhawk as run by Gary Gygax, we are told it was constantly in flux; new areas were being created, old areas were being re-worked, etc.
This is certainly not something that I've paid much attention to in the past myself, but it's something I've included (via the Greyhawk Construction Company) but hardly emphasized in my recent Castle of the Mad Archmage work. But I think it's an important piece of the megadungeon puzzle, as I've discussed in the past. They're not static things; they are always in motion. Not just with creatures moving into new digs to replace ones that have been slain and traps being reset, but the very physicality of the place undergoing change. The pace can be slow, or it can be swift, but in order to capture the true notion of the megadungeon as a constant work-in-progress, it should not be ignored.