Peach's Castle (SM64)
File City (Digimon World 1)
The House of Hades (Hades)
The Normandy (Mass Effect 2/series)
I love hub worlds where you bring characters back from your adventures and they help develop it, and the best example I can think of for that is Digimon World 1 (the game is better remembered as a town builder than a digimon game, which I'm not sure was at all intended).
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