Yaoi?

Yaoi that goes beyond it's genre in my opinion: http://www.mangago.zone/read-manga/haru_wo_daite_ita/
http://www.mangago.zone/read-manga/saezuru_tori_wa_habatakanai/
http://www.mangago.zone/read-manga/castle_mango/
http://www.mangago.zone/read-manga/yuuutsu_na_asa/
http://www.mangago.zone/read-manga/acid_town/
http://www.mangago.zone/read-manga/the_man_of_tango/

Also http://www.mangago.zone/read-manga/love_mode/

I love all of your suggestions! Re read many

Maybe these:
http://www.mangago.zone/read-manga/lovers_doll/
http://www.mangago.zone/read-manga/yume_musubi_koi_musubi/
http://www.mangago.zone/read-manga/nemureru_tsuki/

http://www.mangago.zone/read-manga/brother_x_brother/
http://www.mangago.zone/read-manga/sorenari_ni_shinken_nandesu/
http://www.mangago.zone/read-manga/doubt_nishimura_shuuko/
http://www.mangago.zone/read-manga/toshishita_no_ryuugi/
http://www.mangago.zone/read-manga/saa_koi_ni_ochitamae/
http://www.mangago.zone/read-manga/crimson_spell/
http://www.mangago.zone/read-manga/the_hinanomori/

Dear Green series:
http://www.mangago.zone/read-manga/dear_green/
http://www.mangago.zone/read-manga/dear_green_hitomi_no_ounowa/

the warui series from Sakuraga Mei:
http://www.mangago.zone/home/mangalist/6968/

the series from Fujisaki Kou:
http://www.mangago.zone/home/mangalist/7543/

http://www.mangago.zone/read-manga/endless_world/
http://www.mangago.zone/read-manga/canis/
http://www.mangago.zone/read-manga/yamada_to_shounen/

http://www.mangago.zone/read-manga/sora_o_daite_oyasumi/
very very deep & dark. Will rip your heart to pieces.
http://www.mangago.zone/read-manga/endless_world/
another tragic yet very meaningful beautiful story.
http://www.mangago.zone/read-manga/coponicus_no_kokyuu/
this one requires a lot of attention from the readers. Not only as BL, but it has a very deep story as an individual story too.