Obviously it's the total package, but I guess I like the dungeons best. Those have the biggest impact in my consideration of favorite Zelda games; hence why Twilight Princess is miles above The Wind Waker for me.
However, as I said it's the total package, a game without the overworld would be very boring. It's also where the story is told. This reminds me, I'm so glad Ocarina's original concept, where the entire game was set only inside Ganon's Castle fell through.







