Well, this can be objectively measured so-to-speak.
LoZ's biggest feature was its huge overworld, but the dungeons were also very good and advanced for the time, but this would have to go to overworld,
AoL biggest and most memorable achievements were of their dungeons, or palaces as we knew them. So they would have way better dungeon designs.
ALttP was pretty much equal in design with dungeons and overworld, and both were extremely well-paced and played.
Link's Awakening was very good on all regards, but I think it focused more on the dungeons, as each were unique, thoughtful and overall amazing.
Ocarina of Time is very similar to A Link to the Past in that it was well paced and equal on both sides.
Majora's Mask definitely favors overworld, as that is where the meat of the game is. The dungeon designs were unique and challenging, but also feel sort of rushed and lacked polish
OoS and OoA are equal out each other I think, with exploration, and combat in both terms.
Wind Waker is basically all overworld, WW's Dungeons were very bland and lackluster. Definitely goes to overworld with this one and the Great Sea is quite amazing.
Minish Cap is a unique case. As it's overworld is practically one giant dungeon. So, I think I will put it on the dungeon side. Even if this weren't the case, MC's focus was definitely with dungeons.
Twilight Princess has the opposite problem, the Overworld was bland and lackluster, while the Dungeon designs were very good.
PH favors overworld, and its dungeons were extremely bad.... Overworld exploring is bad too, mind you, but I think it edges dungeons out.
ST features Dungeons, with its most prominent feature being the Tower of Spirits. I love the dungeon desing in this game.
SS definitely has a similar issue to MC. The overworlds did feel like their own dungeons, not that it is a bad thing. SS also had some of the best dungeon designs we have ever had, so it was extremely good and ok for this.
ALBW is very similar to ALttP in the fact that it is well paced, yet I have to give dungeons the benefit of the doubt. They were so unique, so much fun, and very well paced.
I think that currently, dungeons beat the overworld, yet that is something Zelda Wii U hopes to change.
I really hope that it is well paced like OoT and ALttP though, so both can be as equally as great. That would make the most amount of people very happy. I love both equally, for different reasons, and I would love to have that work out equally.