On NGC there's a good RPG called Skies of Arcadia Legends and mostly you recruit people for your ship (they give you special bonuses) but near the end of the game you find this island and set it up as a base, and then you can upgrade it and all your extra crew go there. I really enjoyed it, and it's a really good game (crappy graphics tho).
I also liked upgrading the town in Assassin's Creed 2, tho I know it's not quite the same. I guess I also just like that feature in games.
And older series - well to me - is Heroes of Might and Magic which is more of an RTS/Strategy game but anyway you have to build up your castles to produce new units, get upgrades, and also defenses like moats, towers etc. I only played 2 and 3 with 2 being my favorite but I think the series has some much newer entries. Might be worth a try (if you can get 2 for free online check it out)