This one is possibly rather hopeless and I'm not even sure if I'm posting in the right section, but what the hell.
I'm looking for manga where romance, sex and all that is just a means of storytelling or maybe it's even nonexistent. You know, a story that focuses on conveying a message or exploration of the human mind that just happens to involve gay characters and whether there is romance and/or sex, the focus is on contemplation, dialogue, metaphors... yeah, doesn't really sound like BL, right? I'm just wondering if there's anything like, say, Solanin or even Hourou Musuko where the main character/s is/are gay. Maybe a story of an unrequited love that stays unrequited and enables the narrator to ponder on society or about a coming out without any romance in sight?

As I said, this might be a pretty hopeless case

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LET'S POSITIVE THINKING

New York New York is one of the rare manga that actually made me think about gay community and things they have to go through just to be able to be with the one they love. It's a really touching manga I'd say.
The limits that desire allows us is mostly about the difference between "love" and "desire". That was somehow deep and you actually have to think to understand it. It took me 3 times to read that manga to finally get what it's trying to say.

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K n e e l .... This is the difference between your and my eye-level.
Rai from Noblesse

Innocent (SAKAMOTO Shinichi)? The story itself isn't yaoi, but i'm pretty sure the main character is gay, tho the historical figure he was based on wasn't

You're looking for a yaoi? Because I was reminded of 12 days

A Cruel God Reigns is one of my favorite psychological manga. Visual metaphors abound!

Saezuru Tori wa Habatakanai possibly.

Bannin - some nicely disturbing stuff in here.

Hetalia dj - Arthur in the Dark - nice split personality exploration.

Sakura-Gari - so much tragedy...

Hmm... I don't know if you read Novels, but you should definitly give Utsukushii Koto a chance. Very thought provoking, and not many yaoi novels/manga deal with the crossdressing topic in such a deep and psychological manner.

Thanks for all the suggestions! Some of them were already in my wish list and yep, that counts for the novel too.

If anyone comes across this topic then I'd like to reccomend Hachiue no Juunin - I stumbled upon it by pure accident a few days ago and it really fits the criteria.

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LET'S POSITIVE THINKING

I definitely recommend Endless World! It had me thinking about it for days afterward. Keep in mind that this is not fluffy by any means.

Another manga that has the human condition as a big theme is Akaneshinchi Hanaya Sange; it is deeply philosophical. But be warned that it is on the dark and graphic side. I had to read it a few times to truly appreciate it.