Note - all these are SPOILERY descriptions, since I need to explain how the family finds out.
Shout Out Loud! - son discovers Dad's gay relationship (and yaoi voice-acting job lol!). Dad also discovers son's gay relationship. Sounds unlikely, but is VERY well done.
Omoisugoshi mo Koi no Uchi - so-called "straight" uncle thinks that his nephew's going out with another boy, and tries to be supportive by finding out more about "gay culture" (lol). He actually goes to a gay bar to ask for advice about how to accept his nephew, but ends up being picked up by a man there, who then pursues him. Ironically, at the end of the manga it's the uncle's new gay relationship that is discovered by the nephew!
Spoiled Within Our World - gay twins assault a male classmate and get discovered/ostracized from their hometowns and families. Not "relationship" discovery per se, but... gayness discovery? Lol. Should also add that the twins know about each others' relationships with other guys, and eventually have sex with each other.
Junjou Romantica - main seme's father and brother find out about his relationship with a younger man. You've probably read this one, though.
Adult's Problem - straight son discovers his Dad's relationship with another man near the son's own age, and... panics. HILARIOUS.
The Tyrant Who Fall in Love - the seme's family had found out about his homosexuality (and relationship with another boy) as a teenager, and had completely ostracized him after that. Very sad, but some repair is done to this damaged family in the manga. Largely thanks to the crazily violent uke. Lol.
Morning Kiss - everybody in the family knows that (practically) everyone else is gay.
Home Drama - not blood-related sons, but they do belong to the same family register and know about each others' homosexual relationships.
Yasashiku Toraete - elder brother discovers his younger brother's gay relationship and tries to break it up.
Awkward Silence - I
think the Mum eventually finds out about her son's gay relationship, but she's so darn cute and accepting!
Itsuwari no Daishou - son discovers Dad's gay relationship with a male secretary, and "inherits" that relationship when the Dad is hospitalized.
BLT - Burning Love Twin - more twins that know about each others' gay relationships.
Sex Pistols - most of the families here know and officially recognize the gay and lesbian couples.
Yaizu Brothers Fucking Cool - er, yeah. Pretty much what the title says. All the brothers know about each others' gay relationships; I think they sleep with each other, too.
Trouble Maker - I think the mother and the brother know? Yeah.
Kusatta Kyoushi no Houteishiki - brothers know about each others' gay relationships (eventually).
Most of
Yamada Yugi's mangas have SOME sort of family discovery of the gayness!