I agree with Kishi about the FFIII and FFV maps. I remember both those revelations, the world within a world and the two worlds that merge into one, blew me away when I first got to those stages in the game. Pretty great twists.

Might be an unorthodox choice because it's not really a world map, but I quite liked FFXII's actually. I enjoyed how various locations joined together in ways that you wouldn't know about until you explored them and also how it's only by doing the exploring that you get a full idea of what the world is like. That and the environments themselves were on the whole quite nice to look at and it made exploring that bit more enjoyable, I felt.