
Those were deep and beautiful in my opinion:
http://www.mangago.zone/read-manga/senya_ichiya_shitone_no_himegoto/
http://www.mangago.zone/read-manga/jigoku_meguri/
http://www.mangago.zone/read-manga/hanazono_no_kioku/
http://www.mangago.zone/read-manga/wild_rock/
http://www.mangago.zone/read-manga/vassalord/
http://www.mangago.zone/read-manga/shingeki_no_kyojin_dj_getting_closer/
http://www.mangago.zone/read-manga/soul_kiss/
http://www.mangago.zone/read-manga/koujitsuei_no_tobira/

if you want deep story, my suggestion is to read long mangas not just oneshots or smuts
anyway here's a few of the really good ones i can think off my head right now
http://www.mangago.zone/read-manga/love_me_thru_the_night/
http://www.mangago.zone/read-manga/ai_no_kotodama/
http://www.mangago.zone/read-manga/u_don_t_know_me/
http://www.mangago.zone/read-manga/arashi_no_ato/
http://www.mangago.zone/read-manga/ake_nure_goyou_ni_furu_yuki_wa/
you can also look over my unrequited love list http://www.mangago.zone/home/mangalist/43233/

if you want deep plots my suggestion is to look at long-chaptered shounen-ai more than oneshots and smuts
these are the titles that i can recall in my head right now that have those poignant, heartfelt and oftentimes complicated stories that i think are not that popular
http://www.mangago.zone/read-manga/ai_no_kotodama/
http://www.mangago.zone/read-manga/dear_green/
http://www.mangago.zone/read-manga/soredemo_yasashii_koi_o_suru/
http://www.mangago.zone/read-manga/gives/
http://www.mangago.zone/read-manga/u_don_t_know_me/
http://www.mangago.zone/read-manga/ake_nure_goyou_ni_furu_yuki_wa/
http://www.mangago.zone/read-manga/moshi_koi_da_toshite_sayonara_itoshi_no_my_friend/
you can also go over my unrequited love list, i took time reviewing titles so it could help you choose what you wanted to read
http://www.mangago.zone/home/mangalist/43233/
I like yaoi with good story based ones, with deep plots.. .like seme loves uke so much but uke didn't love back or onesided feelings or whatever.. with deep romance.. some yaoi is just about scenes, i prefer deep story ones. Onegaishimasu!