Here's a couple off the top of my head (hopefully there's at least one you haven't read yet):
http://www.mangago.zone/read-manga/koakuma_no_sanctuary/
http://www.mangago.zone/read-manga/sekaiichi_hatsukoi/
http://www.mangago.zone/read-manga/junjou_romantica/
http://www.mangago.zone/read-manga/yebisu_celebrities/
http://www.mangago.zone/read-manga/the_4th_guard/
http://www.mangago.zone/read-manga/ai_to_yokubou_wa_gakuen_de/
http://www.mangago.zone/read-manga/kachou_fuugetsu/
http://www.mangago.zone/read-manga/ze/
http://www.mangago.zone/read-manga/love_mode/
http://www.mangago.zone/read-manga/honey_boys_spiral/
http://www.mangago.zone/read-manga/kibun_wa_joujou/
Series:
http://www.mangago.zone/tag/warui+series/
http://www.mangago.zone/home/mangalist/5918/
http://www.mangago.zone/home/mangalist/56512/
http://www.mangago.zone/home/mangalist/53655/
And a list of yaois and their spin-offs:
http://www.mangago.zone/home/mangalist/82895/
Anyone knows yaoi manga (or maybe list) where there are multiple couples who somehow know each other?