hey slushies! 😀
So I just read one called Domino Naranai and I loved the way that there was the first story and then in the second side characters became couples :3 It can have 2-3 stories, and in each one you notice the side characters and they aren't involved much, but then there's another part where it focuses on them.
oh yeah! NO SHOUNEN AI!!! Must have lemons goodness XD
PLEASE don't mention Junjou romantica DX I hate that manga >.>

Oh, what a wonderful life it is to those who make it wonderful.

Hand Which first stories. I know a lot of manga with that setting, but I can't remember right away. Otona Keikenchi has one too... Mainichi Seiten mangas, it's a collection and it has 6 different stories about the same househood. Kibun wa Joujou! too and Room Share, if I remember right... Oh yeah, Sentimental Garden Lover somehow fits and Konna Otoko wa Aisareru and its sequels Himitsu no Yoasobi&Ai no Kotoba mo Shiranaide. Twin's Labyrinth! Hm, I can only remember these for now.

ahh the famous warui series is a definite! (the art is gorgeous)
warui koto shitai

lιvιɴɢ ιɴ α yαoι woɴderlαɴd
-QaF-

I love these kinds of manga too. I'll list what I can remember right now, and try to come up with more later.
Single volumes
Dolce
Kyou, Hana no Gotoshi
Ikenai Otoko - second story tells the backstory of the other couple
Mezase Hero!
Oujisama Game and sequels
Three Wolves Mountain - the second couple is unusual even by yaoi standards
Kimi wo Mukaeni
Mae yori mo Dare yori mo
Tsuyogari and sequel Hidoku Shinaide [added]

Side characters have to wait to get their own volumes
Ubawareru Koto Marugoto Zenbu - continued in Suki Toiunoni Nazekashira, where the main story is about a side couple from the first volume

All these are set around the same restaurant:
Tenshi no Tamagoryouri
Kekkon Dekinai Otokotachi
Sunao ni Narenai Otokotachi

Akuma wa Hohoemu - the main couple first appear as side characters in Kawaii Akuma and Itoshii Akuma

Meguriau yo Baby and Don't Cry Baby

Characters that appear in one volume get their own stories in another:
Te o Tsunaide, Sora o
Amayakana Toge
Aisanai Otoko

Takaga Koi daro - loser in love triangle gets his own story in Aiso Tsukashi

Tsumasaki ni Kiss - loser in love triangle gets his own story in Gravity Eyes

You could also try a genre search on the category 'Collection of Inter-Linked Stories' for more.

I actually just read one like this ~ it was pretty cute and had great art Kimitachi Otokonoko

1K Apartment no Koi