Abarenbo honey
Both couples in this story are adorable in their own ways. The first couple, Kuma and Hachi are a more stereotypical omega x alpha couple. Their initial encounter is a little questionable, but they eventually become a sweet and devoted couple, supported by Hachi's family. The second couple, Mitsurou and Suzume are less typical. Suzume, the alpha, might be younger, but he understands how important Mitsurou's independence and control over his body is to him and doesn't take advantage. He waits for years and continues to ask consent. Seriously, if only more omegaverse stories could be like that! And it isn't any less wonderful for the consent. If you are looking for a sweet omegaverse story, there are few on par or better than this.
Haikyuu!! - Do You Know Anything About TPO, Kageyama-kun?! (Doujinshi)
Koi wa Ina Mono Myouna Mono
A rare yaoi manga where the seme, despite wanting the uke terribly, actually acknowledges forced sex = rape = bad, and continues to ask for consent. The actual premise is funny, with the uke receiving dreams of the future and seeing himself with this guy and refusing to accept it. I loved the two families and the glimpse into the future. If you actually want to see their first time together, it's ch 7 in Aruji No Oose No Mama Ni. Overall, if you don't mind super tsundere ukes and like fated lovers and devoted semes, this is a great manga.
Yuuhi ni Fureru Sono Mae ni
The first story is my favorite. Two roommates/housemates gradually fall in love with each other as the seasons change during their 4th year of college. One is an architecture student who doesn't connect with his father's new family and the other a painter who is almost always cheerful but also has (minor) angst with his family. Their connection was sweet and sincere and you wish you could see them in 10 or 20 years painting and building homes!
Ai Wa Chitto Mo Rakuja Nai