Tsuki wo naite hoshigaru kimi
Ten years after leaving his hometown for Tokyo, Mitsuki reconnects with Kiyozi, his best friend from childhood. They fall into a physical relationship, but Kiyozi is keeping something from Mitsuki, who feels used until he speaks with Kiyozi's ex-wife. Other commenters seemed to hate this story, but I truly enjoyed it. It's slow and subtle, but it's about second chances and the stupid things we do to protect ourselves from getting hurt.
Amadare no Koro
Two boys in the sweetest and purest love elope in middle school. In the final chapter, they comfort a friend who has his heart broken.
Mousou One Room
Manga artist in love with his younger brother's friend gets the shock of his life when he shows up at his front door and asks to stay. Neighbors and childhood friends start dating.
Kore ga Koi!
A guy forced to crossdress as a penalty game meets a teacher who saves him from assault. Childhood friends in disgustingly sweet love have their first time together. Childhood friends discover they are neighbors and in mutual love.
Me o Tojite 3-byou dj - Me o Hiraitemo, 3 Senchi
DJ for the one about the childhood friends in mutual love who missed confessing to each other because one transferred schools. This is also included with the main story on this site.
Natsukage Ni, Sayonara
Two boys who meet through a part-time summer job fall into an innocent first love. (First few & final chapter) Childhood friends who discovered intimacy with each other haven't spoken for five years after they were caught & are reunited.
Futari Bocchi no Shokutaku
A lonely man takes in a man without a home to return to, and over half a year, they fall in love. Gentle, subtle, and incredibly moving. Childhood friends start dating and have jealousy issues (and very long bangs).
Kazoku Gokko (KIKUYA Kikuko)
After his childhood friend (and unrequited love of his life) is left by his wife, Toki moves in to care for him and his young son, Akira. We come into the story three years later, when they have settled into a comfortable life that neither man wants to give up despite family pressure.
Dare ga Omae wo Sukida to Itta
Super short but enjoyable oneshots. - Kid with major crush keeps meeting his crush's milestones and they finally get together - Two guys meet up at a reunion and become roommates; later, the teenage son of one assaults the other, but it's what they need to realize their feelings. I actually liked their story the best. - Newbie at work has to track down the old manager, who'd been in a relationship with the president's son and had to resign. - Strong friendship story about a part-timer who works around the clock to make ends meet and is picked up every morning by his manager, whom he originally knew only by his shoes - Two men in a long-term affair suspect they're being followed by a detective hired by one of their wives (they are divorcing)
Koi Wa Amai Ga Shoppai Ga