Oh my these types of yaoi are my favorite!
In my eyes, the yaoi which touch on the more disturbing side of human nature are much more realistic, and evoke more "feels". Some may be too disturbing though, so be warned.
Yuuutsu na Asa (MY FAVORITE. I CRIED SO MUCH)
http://mangafox.me/manga/yuuutsu_na_asa/
J no Subete (really messed up, but you feel so much heartache for the characters TT^TT)
http://mangafox.me/manga/j_no_subete/
Saezuru Tori wa Habatakanai (okay this one is a must read)
http://mangafox.me/manga/saezuru_tori_wa_habatakanai/
Doushitemo Furetakunai
http://mangafox.me/manga/doushitemo_furetakunai/
Ouji no Hakoniwa (pretty sad as well)
http://mangafox.me/manga/ouji_no_hakoniwa/
Not equal (has uh.. a strange sort of incest)
http://mangafox.me/manga/not_equal/
Zankoku na Kami ga Shihai Suru (old, but really good)
http://mangafox.me/manga/zankoku_na_kami_ga_shihai_suru/
Nanadome no Gomenne (incest - freaking hurt my heart reading it though. also, it is a oneshot)
http://www.mangahere.com/manga/nanadome_no_gomenne/