Dont read the rest if all you want is this answer: You can't go wrong with any mainline zelda game (3D or top down)
My favorites are top down zelda games thanks to amazing puzzles (also some of my all time fav games) so I would say the most popular one which is Link to the Past. My favorite is Oracle of Seasons though, absolutely brilliant game.
As for 3D Zelda games I'm prob not the right person to ask but I'd say Twilight Princess for Gamecube. I didnt care for Ocarina of Time or Skyward Sword. They were ok but not something that I would go back to any time soon. Wind Waker is good and beautiful.
So in order this is how I would rank them
Top Down(Just bought Link Between Worlds so no opinion on it yet)
1. Oracle of Seasons
2. The Minish Cap
3. Link to the Past
4. The DS franchise (meh)
3D Zelda
1. Twilight Princess
2. Wind Waker
3. Ocarina of Time
4. Skyward Sword
If you just want to go with the most popular it would be Ocarina of Time and Link to the Past. I think that is partially because of nostalgia though.
