Hmm, its a hard call. How about top five, in no particular order?

1. Legend of Zelda: Link to the Past - mmm, psuedo-isometric goodness
2. Cloth map form Ultima Online - just good stuff
3. Hobbit - I agree with what others said, I studied that map to no end
4. Can't remember the name - but it was this insane city map from Warhammer RPG some industrial city by the river. It was posted around here once. Mind blowing the amount of detail and scale.
5. The Freeport map - brilliantly done.