Seifuku wo Matoeba, Umaku Uso ga Tsuketa no ni
Once inseparable childhood friends have become rival pilots, but it's really a bunch of unresolved feelings going back to their middle school days. Things work out just fine.
Saburina
Middle school friends who attend separate high schools still ride the bus together every day.
Kakko Warukute Kakkoii Kimi
This is so cute. Childhood friends get to high school, and then one starts to pull away from the other! He's upset about something ridiculous (his height) and eventually everything works out.
Tight Rope
Childhood friends in a close relationship have to decide if they want to be together for life or part ways when Ryu accepts being the fifth heir in a yakuza family.
Usotsuki Wa Dareda
After his best friend Hiromu finds him with another boy in high school and calls him disgusting, Ichi loses touch with him, though they live in the same building as adults. When Ichi's grandfather comes to visit, Hiromu comes back into the fold, and he and Ichi have to come to terms with their relationship fallout.
Hana No Miyako De
This ties into Hana no Mizo Shiru and tells the professor and Misaki's grandfather's story. It will probably make you cry. Misaki and Arikawa are in this as well, and we get a little relationship development to make up for the tragedy in the first chapter. ETA: Maybe they saw one another while Akira was still alive, after his wife had passed. I like to think they wrote each other letters and remained good friends, and maybe even stole away for time together sometimes, hopefully with the full knowledge of their partners.
Tonari No Usotsuki
The second story is the best one. Two boys forcibly separated two years ago find one another in high school.
Toritome no Nai Koi no Shi
A man wakes up to find a hole in his chest.
Ichi Ni no San!
Three friends - two boys and a girl - have been friends since childhood. You can guess which two (eventually) hook up. Kudos to this story for a charming, lovely female character. She is precious and I Love Her.
Takaramono wa Hako no Naka