Since I'm God-awful with names, the only ones I can think of atm are:
http://www.mangago.zone/read-manga/houtou_musuko_to_sewagakari/
http://www.mangago.zone/read-manga/raising_a_bat/
You might already have read them, so I'll let you know if I remember any others~
Nirameba koi
Mousou Elektel
Bagjwi Sayug/Raising a Bat (not yaoi, but I definitely recommend.)
Calling (Ootsuki Miyu)
Dokidoki Renai (also not yaoi).
Mad Cinderella
All I can think of, atm.
'Aaye~ The family part in Raising a Bat comes down the line, but there's hurt in between there LOL. I love it nonetheless though.
I also remembered this one, but it's omegaverse, so if that's not your thing, proceed with caution http://www.mangago.zone/read-manga/bokura_ga_tsugai_ni_naru_made/
(also sorry if this is a double post, I'm not sure if I submitted it before or not LOL)
http://www.mangago.zone/read-manga/u_don_t_know_me/
http://www.mangago.zone/read-manga/sannin_gurashi/
http://www.mangago.zone/read-manga/ani_no_hanashi/ this one is sooo sweet, it's told from the perspective of the younger brother of the gay guy
Father, I have a confession... I have a major bias towards yaoi where the families of one or both of the guys are introduced to the other for better or worse..... I confess my bias gets even bigger when the family is supportive.
Due to this bias I'd like to yell this request into the endless void of the internet:
Is there a yaoi you love that depicts a familial relationship (non-incest being the one stipulation) that is positive on a character? Whether it be apathetic acceptance ("honey I've known since you were 5ish, what do you want for dinner" - my exes coming out story) or active acceptance like in Honto Yajuu, I just want the fuzzy feelings.
Thanks if you read this wall of text (although I'm pretty sure this will be lost to the winds of mangago forums quickly) and thanks for any suggestions you may deliver I'll be sure to read and add to my list. From one gay fudanshi to the yaoi community thanks :D