My ranking has changed a bit since this post. Most notably, my placement of Skyward Sword is a good few spots lower now.I'm currently replaying all the Zelda games in release order, and I have not yet played Breath of the Wild, so expect my list to change in the near future. Already, the first two games have risen on my list because I had a lot more fun with them during my current playthrough.
Consider this a "before/after" kind of thing. I don't expect MM or TWW to move spots, but I think all of the others are relatively interchangeable.
Majora's Mask - My absolute favourite Zelda game, and I don't see that changing unless BotW completely blows me away.
The Wind Waker - Played this game a thousand times, never get tired of it.
Skyward Sword - Probably the most controversial placement on my list, and I think it's the one that's most likely to change a lot when I get to it again.
A Link Between Worlds - Might move up or down a spot, but I really don't expect this one to change all that much.
Ocarina of Time - See, I think this is a far better game than SS speaking objectively, but I tend to have more fun with the latter. The thing that will probably make this game go up is that it is far more replayable than SS.
The Minish Cap - This game and AlttP are relatively interchangeable at this point. I've only played through TMC once though so we'll see if this placement changes substantially upon my next playthrough.
A Link to the Past - Classic Zelda game. Perfect blend of difficulty, story, and combat. May move a little bit, but will likely remain in the High Tier (currently playing through again).
Oracle of Ages - Another game that I've only played once, and will probably not change much. I loved it when I played it!
The Adventure of Link - Just finished this game for the second time, and upon my second playthrough, it jumped substantially (see my sig for old ranking). I found ways to appreciate this game once I had really gotten into it that I had failed to see before. I genuinely enjoyed it, which was something I never thought I'd say about AoL. This one actually has the potential to break into the high tier once I play it again.Low Tier - I think these games will likely remain relatively the same. I don't really see my mind changing much upon playing them again.
Twilight Princess - I find myself liking this game less and less every time I play it, but I can't really figure out why. I loved it the first time, and there are many many things in it that cause me to consider it a genuinely fantastic game. But there's just something about it that makes me hesitant to replay it. Maybe I'll have a newfound appreciation for it when I get to it again, since it has been a few years since I've played it.
Spirit Tracks - This is one that is likely to go down in my list. I really like this game, but there are a lot of things in it that I think could have been done better. I think it will always be higher than Phantom Hourglass, and it will probably always stay Mid-tier, but I don't think it is going to be this high up when I play it again.
The Legend of Zelda - Man, I used to get really bored when I played this game, but I've recently found ways to really enjoy it. It was really close to the bottom of my list before (see my sig), but it has definitely risen in the enjoyment factor for me. Still, I've only beaten it twice, and I haven't mastered it yet, so maybe when I get really good it will go even higher. While it's not there yet, I can see this game jumping way up to the mid-high tier.
Oracle of Seasons - This one is kind of complicated to me. I haven't decided if I love OoS or if it's just OK. I have only played it once though, so I'm sure my opinion on it will change. I absolutely adore its other-half, and I did like this game a lot upon my initial playthrough, but I think its relative focus on combat doesn't really work for the top-down 2D perspective (in contrast to the more puzzle-focused Oracle of Ages). I think this one will most likely go up on my list though when I play it again.
Tri Force Heroes - Genuinely fun multiplayer experience, and I really appreciate the "Drablands Challenges" adding many new ways to play the game. The problem with this game, ignoring the god-awful single player mode, is that there isn't anything truly mindblowing about it. The totem mechanic is cool, and I do love being able to play with friends, but overall the gameplay is relatively simple and the game gets rather boring and uninteresting after a while. It had a ton of potential, but I feel like it just fell short.
Phantom Hourglass - This one hurts a bit to tell the truth. I really really really want to love it, but I just can't bring myself to do so. I was really excited when I saw that we were getting a DS Zelda game, especially considering it was gonna be a sequel to what was then my favourite Zelda game. Then I got it, and it fell below my expectations, which was a real shame because it had a lot going for it. Ignoring the fact that it's too easy, the sailing was even more tedious than in its predecessor, and the Temple of the Ocean King, while a cool idea on paper, didn't work for me. Plus some of the controls were kind of weird (and thankfully most were improved in its successor), which lessened my enjoyment of the game even more. While I do have fun with it, I've always seen it as just being sort of OK. Not great, not bad. Just good.
Four Swords Adventures - I used to absolutely love this game, but it drops on my list every time I revisit it. It's fun the first time, and it's got some really great puzzles in it, but it's just not that interesting, and its replay value is severely lacking. There's some interesting level design, but I don't like how all the levels are disconnected (which is a problem with all of the Four Swords games, including TFH). It's also really easy. There are things about it that I love still, but I just don't enjoy it like I used to.
Four Swords - Basically suffers from all the same problems as Four Swords Adventures, but adding on an extreme inaccessibility issue. I really don't have a whole lot to say about this game. I do like it, and I enjoy playing it, but I think as a Zelda game, it really falls short.
I've been contemplating where to put Breath of the Wild on this list. It's a great game for sure, but I struggle to believe it's going to be very replayable for me. Right now I'd probably put it right below A Link Between Worlds but it's so different from all the other games in so many ways that it makes it hard to compare it to the other Zelda games. And I think once I play through it a second time, depending on whether or not I'm proven wrong about the replayability, it could either move up or down.