I haven't finished BotW yet, so I haven't finalized it's placement in my list yet, but as it stands, it goes as this:
1. Wind Waker - favourite game of all time. Love pretty much everything about it, even the sailing and Triforce Quest.
2. Twilight Princess - 2nd favourite game of all time. Has my favourite dungeon selection, including my favourite dungeon in the series (Snowpeak Ruins), Midna is the best sidekick, excellent combat. Only things that bring it below WW is its slow start and I don't think its look has aged nearly as well.
3. Ocarina of Time - 4th favourite game of all time. Got me into gaming. 2nd best dungeon selection. Most replayed game. Still love it to this day. Deserves all the praise it gets.
4. Skyward Sword - Very slow start has delayed me from replaying it, but everything else is wonderful. Great dungeon selection, motion controls work well, best version of Zelda next to Tetra, fun sidequests.
5. Link’s Awakening - my favourite 2D entry. It's simple, but elegant. World design is great, dungeons are fun and inventive, fantastic music.
6. A Link Between Worlds - best 3DS game. Love the open ended structure of it in the 2nd half, dungeons are mostly great, looks good. Thought I was gonna hate it after hearing about the painting mechanic, but ended up really liking it. Need to get around to replaying it.
7. Breath of the Wild - 7th place seems right for me. Best adventure aspect in the series, lots and lots to do, but dungeons bring it down for me. Not a fan of the voice acting either.
8. Minish Cap - Unique hook, great art style, fun dungeons. Overall, very good.
9. Phantom Hourglass -Has its fair share of problems (namely Temple of the Ocean King), but still enjoyed it, especially as its a sequel to WW. Linebeck is a fantastic character too.
10. A Link to the Past - one of the first games I ever played. Not quite in love with it as other people are. Objectively, one of the best in the series, but subjectively, don't see it as a highly. Still, wonderful music and graphics, dungeons still mostly well designed (hate the ice one though), great evolution of the series.
11. Oracle of Seasons - consider this the description for both Ages and Seasons. Both really good for the GBC. I liked Seasons' mechanic a bit more, and enjoyed its focus on combat more. Jabu Jabu from Ages annoyed me a lot too.
12. Oracle of Ages - see above
13. Majora’s Mask - similar to Link to the Past in that don't like it as much as most. Dungeons ultimately made me not like it as much, as I only really enjoyed Stone Tower, and actively despise everything about the Great Bay Temple. Didn't really do many sidequests, which probably didn't help.
14. Four Swords Adventures - played only in single player. Still decent fun, but really weird.
15. The Legend of Zelda - Great start for the series, but as someone who didn't grow up with it, later games just did everything so much better, namely dungeon design.
16. Zelda II: The Adventure of Link - hard as hell, never really got into it. Still admire it for what it did.
17. Spirit Tracks - my least favourite core entry. Hate the ghost Zelda mechanic, the train, while decently fun, kinda ruins the adventuring aspect, flute irritated me to no end, dungeons all forgettable. Just not much I really like about it.
18. Four Swords - it's fine, but I only ever played the 3DS version since it allowed single player. Too short, kinda repetitive, nothing particularly "fun" about it