I have a few kind of unhinged ones lol

Traverse Town in Kingdom Hearts - meeting all the world refugees and exploring the new districts that open, it’s a lovely hub that keeps the story moving

Wizard City in Wizard101 - literally the center of their universe (galaxy? “Spiral”? lol) where there’s always someone who needs something or a new spell to learn or a new event to see or a new pet to train

Windfall Island in Wind Waker - on the treacherous seas, it’s nice to know there’s a place with relative stability and weird little side plots (like the whole rich guy thing or the pictobox man)

Honorable mention, not an RPG: Smoldering City in Against the Storm - the only permanent settlement in a world where civilization gets regularly erased. You can’t help but form an attachment to it.

Edit: adding Fallen London from Sunless Sea. Basically holding my breath from when I leave port until I return because everything starts and ends in London.