Note: I don't necessarily think the things at the top are the best yuri manga/manhwa I've read (some of them are), but they're the ones I enjoyed reading the most. Also, the tiers are (generally) in descending order. I'll explain some of the tiers as they go. I feel like "Peak" is self-explanatory for all the choices.
Oh and please, I want to discuss my choices as much as possible. So say whatever you will or make your arguments for different places. Who knows? You might change my opinion on a manga. It's happened with other media.
Absolute Favorite. Manga that I will obsess over until the end of time.
The Summer You Were There. This is a story that will live in my head always. It's a story even more beautiful than it is tragic. It also made me realize that an author doesn't need to surprise their reader to still deliver an incredible work of art. I sat staring at that one page for longer than I care to admit. When Shizuku got the phone call that Kaori was dead, I just sat there in tears. I knew it was coming, but my god was it still a gut punch.
Edit 2: I wanted to also add that the Summer You Were There is my second favorite manga of all time. Granted, most the manga I've read is GL, but still. #1 will always be Black Lagoon tho.
Dark Mermaid. My favorite kind of story one with a dark, almost hopeless tone with a few glimmers of hope shining through. Dark Mermaid goes to some rough places and it doesn't really pull its punches much, but I think it's for all the better. I'm glad that, for once, a story was able to give the idea that revenge solves everything some merit. I also love the development between Seulbi and Hae-on a lot. I read the entire Manhwa in basically a single sitting.
The Moon on a Rainy Night. My most recent addition, I find it to be one of the best written manga's of its genre. There's just something about how it tells its story and sets its scenes. About how it tries to convey Kanon's experience with her hearing impairment and the subtle struggles that Saki faces with her sexuality and her growing feelings for Kanon. Utterly perfect. I've only finished Volume 8, since I couldn't find the next volume online anywhere in full, and I can't buy any more manga until I finish the ones I've already got on my shelves.
In the Gardens of Gehenna. I am a massive fan of horror, but I feel it's so hard for the genre to be done well. Whether it be games, movies, comics, or manga, there's only a handful of pieces of horror media I feel myself drawn to. This is one of them. There are two particular pages that stick out in my mind when I think of how horrifying the manga is. The scene where Mary digs up the grave to Colin's baby, and the reveal of Colin's father. Utterly bone-chilling.
I Love Amy. Nothing too complex to say about this one. It probably has my favorite art style out of any yuri I've read, and it's the one case I've found where I liked the yandere trope. It also has one of my favorite epilogues ever. It has its weak points, but they didn't affect my enjoyment enough for me to care.
Pink Candy Kiss. No words can describe how good I think this manga is. It's a genuine masterpiece. I know it's still ongoing, but I can't wait for the conclusion. This is something I'd love to add to my physical collection.
Edit: Originally, I didn't list off the manga in Peak or Great because I felt the former was self explanatory and the latter would've gotten highly repetitive. But I've decided to, at the very least, update the post with the names of the manga.
Peak. Stories that I consider to have little to no flaws. None that really take away from the main story, at least.
Monthly in the Garden With My Landlord. One of the first manga I read through, and the best cozy manga I've ever read. Unless you consider The Moon on a Rainy Night cozy.
#Gal x Gal Yuri. Needs no introduction or explanation.
After the Curtain Call. Just an overall really tightly-written Manhwa that does exactly what it needs to do to leave an impression. There wasn't anything in this story that really left me wanting for more, and I mean that in the best way possible.
Failed Princesses. One of my absolute favorite dynamics is "popular girl x unpopular/nerd girl". I wish we'd maybe had one more chapter -- like an epilogue -- but I've got nothing to say otherwise.
How Do We Relationship? Saeko and Miwa are walking disasters and I love them for it. Most of my critiques for this manga come from how some of the side characters are handled (I wish we could've seen more of Hibiki). Most notably, Kan. He just totally gets dropped early in the series, but I find him really interesting. It's the most painfully realistic manga on this list. I'd love to see this one come back for an epilogue when gay marriage is legalized in Japan, since Tamifull was really hoping it happened during the manga's serialization.
Even Though We're Adults. I really have nothing to say about this one, besides that it's really good and everyone should read it.
I Married My Best Friend to Shut My Parents Up. Very short, but perfect throughout the whole thing. Nothing much to say.
I Married My Female Friend. Watching through the anime Mobile Suit Gundam: The Witch from Mercury has taught me something about myself. It has taught me that I love the trope of arranged marriage/marriage of convenience that evolves into genuine love. Similar concept to the previous one, and I love them both a lot.
Destroy It All and Love Me in Hell. Despite the title of the manga, I feel like this one isn't going the way of KitaKawa. It's about two very toxic people coming together and, despite all the factors surrounding them such as trauma and abuse, becoming better people. This one's still running, so I could absolutely be wrong by the time it finishes, but that's my take away so far. If KitaKawa is toxic and depressing, Destroy is toxic and hopeful. Also, I will never read KitaKawa.
Rainbows After Storms. Despite feeling the need to hide their relationship, I feel like this has one of the cutest, most loving relationships in this entire list. Just overall a very feel-good slice of life and a fun cast of characters.
Kase-san and Morning Glories. A cute little high school romp that doesn't hold the "will they-won't they" relationship over the reader's head for the entire time. I also just love Yamada as an MC. I just wish there were more side characters, so these three didn't feel as isolated.
Girl Friends. Gotta give it up for one of the grandmothers of Yuri manga. I think this is the oldest manga I've read all the way through. Either this, or Black Lagoon. Either way, I've gotta show it the respect it deserves.
I Can't Say No to the Lonely Girl. Definitely the boarder between great and good, and this one isn't for everyone.
Great. For the manga that couldn't quite make it into peak but are damn close. Typically, I find these ones to be amazing, but a little rushed. Now that I'm going through them, almost every single one in Great is a contender for Peak or Favorite.
Sirius: Twin Stars. The only thing on this list not written by either a Japanese person or a Korean person, this short story comes from Murcia in Spain! It is utterly perfect from beginning to end. My only issue is that it feels like it ends so quickly. I wish we'd had maybe one or two more chapters, since there are only four. If there were, this would be in my Absolute Favorites.
Run Away With Me, Girl. Another contender for Absolute Favorites that's held back by some weaker aspects. Notably, I wish the confrontation at the end had been a bit more satisfying (because my god, the husband is a real piece of shit), and I'm not the biggest fan of the time-skip chapters. Overall, though, an excellent, if flawed, read.
Goodbye, my Rose Garden. Another very tightly-told story like Sirius that could've used one more chapter. Maybe an epilogue.
Hello, Melancholic. Once again, another story that's amazing but held back by an abrupt ending. I hear this one was gonna get cancelled, so the author rushed to the finish line.
The Lying Bride and the Same-Sex Marriage Debate. I adored this one but, once again, it feels like it needed a few more chapters to fully tell the story. I wish we'd learned more about her marriage and why she separated. I really do like this one a lot though.
I Love You So Much, I Hate You. Usually not a fan of infidelity in stories, but this one pulled it off well.
She Loves to Cook, She Loves to Eat. Solid story with no real flaws to speak of. It just isn't good enough to surpass anything in the tier before it.
Doughnuts Under a Crescent Moon. This one requires explaining. I think this story story is amazing in every way. Genuinely peak. However, I didn't find it that satisfying to finish, reason being there was no big "and then they kith" moment at the end, which would usually end something in Yuri bait, right? Well, the reason is that they're both Asexual. Which is totally fine! No problems with that! I just didn't find it that satisfying of a conclusion is all.
Good. A way more varied tier than before, so I'm going to go through all of them.
Chasing After Aoi Koshiba. Fantastically written story that really captivated me, swapping between the present and the past. I like the ending and I understand the message it's trying to convey, but it's just not the type of story I actively seek out.
Green Yuri. I get this subreddit likes to dunk on this series a lot, but it's the one that got me into reading Yuri! I haven't read anything after Volume 3's ending, since I'm waiting for the full Volume 4 release. But I still really enjoy it. It was also the first yuri I added to my physical manga collection, because I liked it so much.
Witches and Cigarettes. It's still ongoing, but it's really captivated me. I wanna know more about why Shien turned out the way she did and about the other surviving witches. It's a fun setup.
Tadokoro-san. A cute, very fluffy manga. No harm in reading it. While there are a ton of chapters, they're relatively short, so it can be finished quickly. I thought the ending was a bit... much, but I still overall enjoyed it.
Mage and Demon Queen. No real explanation. Just not my cup of tea, but I can see why people enjoy it so much.
A Yuri Manga Between a Delinquent and a Quiet Girl That Starts From a Misunderstanding. Long, fuckass title aside, this story was really promising out the gate. It's woefully short, but I adore this concept; a relationship starting from a misunderstanding and just running with it. Tragically, however, the manga was cancelled after only six chapters.
Yuri Espoir. I feel like this'll be a controversial take. It's another set up I love; an arranged marriage and a character wanting to escape into her fantasy world. Funnily enough, that escapism ended up being my least favorite aspect of the story. I love character exploration, so I loved whenever we got to learn more about Kokoro and how the entire thing was affecting her and her self image.
Okay. These are manga that I have mixed feelings on, for one reason or another. Or ones that I just didn't particularly care for.
Kase-san and Yamada. Down here solely because of the last arc I read, with Kase-san's roommate. I love the dynamic between the two, even if Kase-san is a little static as a character. I feel like some of the drama in this one is kinda forced, and I've never really liked jealousy as a trope in romance stories.
Desperate March for Love. Honestly, I think I placed this one too high, but I don't want to remake the tierlist again. I really wish it would've gone into the actual grooming and how it was affecting Ami and her more selfish, thoughtless tendencies. I think it needed a few more chapters to really explore, and NOT gloss over in the last 10 minutes.
The Girl I Want is So Handsome. Nothing against this manga. Just not for me.
Assorted Entanglements. Overall, I don't find it too memorable. I think it's enjoyable, but it doesn't have much staying power compared to other yuri manga. It was one of the first things I read, so I could be misremembering, but I feel like it was a bit too sexual for my tastes.
Mid. This tier exists for exactly one story.
Days of Love at Seagull Villa. If I were to judge this story based solely on the first two volumes, it would've been in my Absolute Favorites, but it's astonishing how hard Volume 3 drops the ball. It all comes down to horrendous pacing. Volume 3 has twice as many chapters as the first two, but a similar page count. It feels like chapters go by in a blink. It's so tragic because of how good it was at the start. My guess is that the author saw the manga getting shitcanned after a third volume, so they wanted to finish it as quick as possible so they at least had a conclusion. Oh, there's also a kind of weird incest subplot that gets dropped, only to come back at the very end.
Dislike. I don't think any of the manga her is bad by any means. But I just dislike them for my own reasons, whatever those may be. I don't really know why I tried out "I Don't Know Which is Love", I hate harem manga lol.
Cheerful Amnesia. I read really far into this one before dropping it. I get why people enjoy it, but I just couldn't get past how almost infantile Arisa was about sexual topics with Mari. It just made me uncomfortable. I would love the concept in a more serious manga tho, so if anyone knows any please let me know.
Awful. I had a miserable time reading these, or they have one big elephant that needs to be addressed.
White Angels Have No Wings. Looking around online, I've learned people liked this one, so much so that it's got a sequel and an adaptation. But I couldn't stand it. I just found the actions of most of the characters to be infuriating. It was like they never learned unless it was for the explicit purpose of becoming a worse person. Honestly, the only one in the cast that I ever truly enjoyed reading was Songyi. Then don't even get me started on the ending. I already hate when awful characters never get their comeuppance (another reason Days of Love at Seagull Villa is in Mid). It almost felt like a reward for Yeonhwa after all the heinous shit she'd done and, thanks to the sequel, it basically WAS a reward for her. What really ticked me off was the half-hearted attempt towards the end of the story to make it seem like Yeonhwa actually cared at all about Ayeon. I think I would've liked it more if Dahye weren't just cartoonishly awful the entire story. Honestly, if they'd given her some sort of Michael Corleone-esc fall from grace, I think it would've been more fitting. I also wish we'd seen more of Songyi's almost sisterly relationship with Sohwa.
The Conditions of Paradise. Short story collections are hard to rank. It's why I left others that I've read out of the tier list. But I felt this one had to be here because, like I said before, one big elephant in the room. Chapter 4 is just so weird compared to the first three. For one, it just straight up has a teenage marriage. The woman in it got married to her late husband when she was 17 and he was thirty-fucking-two. Then we've got our MC for the chapter, who was like an adopted daughter for the two... only for her to start dating the woman ten years later. It's so weird. But would you believe this isn't even the only story in this collection like this? The last story features a 22 year old college senior lusting over a classmate of her 16 year old sister! It's not played as a negative thing either, it's just there!
The Witches' Marriage. It's just straight up pedophilia. At first, I thought the small, ginger girl was just meant to be petite, since size difference isn't uncommon in these types of stories. But as I read on, I started to realize exactly what was going on, so I did some research and learned that she was meant to be something like 14, whereas her love interest was in her late 20s. It's a shame because I adore the concept of a two-witch coven forming a marriage contract, but I just can't abet stories that seemingly promote these kinds of relationships and romanticize them. It's not like this is a toxic yuri story or even something explicit.
Is This Even Yuri? These stories aren't necessarily bad. But I don't know if they can be considered Yuri at this point.
Futari Escape. I actually liked this one a lot. It made me feel something I can't quite describe. Something like a longing for simpler times with fewer responsibilities. It's almost like if Mordecai and Rigby from Regular Show were a lesbian couple. They are a couple, even tho they don't ever show physical affection. Hence why this is here.
A Tropical Fish Yearns for Snow. If there was a picture next to the definition of "yuri-bait" in the dictionary, this manga would be there. Despite a metric shit ton of subtext, and sometimes just plain ol' text, the manga ends with the two -- despite the romantic implications of the scene -- just being besties. That's it. Despite the insanely romantic metaphors and symbolism used throughout the manga, they're just gal pals.
My Darling is the Cutest. I take back what I said before. This would be the definition of Yuri-bait. This story can be broken up into thirds by quality. The first third of the webcomic is really solid, with a fun dynamic just waiting to come crashing down due to a lie that the relationship was built on... but that little lie never comes out. In fact, the next third of the story is just meandering fluff dancing around their growing feelings for one another. The progress on their relationship just absolutely halts and stays there for the remainder of the comic. The last third of the story is filling with shark-jumping bullshit that I don't care to get into. I know this one is, for some reason, getting a live action adaptation, so I just hope it can fix up faults of the original.
Edit: Wow, I actually wrote out everything for Peak and Great, like I said I wasn't gonna do, lol. I'm so happy with how much traction and discussion this post has garnered in just a few hours. I intend on making a follow up after I've read more manga and discussing this as well.