I highly recommend them all. I'll let you know if I think of any others.
http://www.mangago.zone/read-manga/watashitachi_no_shiawase_na_jikan/
http://www.mangago.zone/read-manga/bokurano/
http://www.mangago.zone/read-manga/a_lollipop_or_a_bullet/
Manga:
Fullmetal alchemist
Death note
Sakura gari
Nana
Shigatsu wa kimi no uso
Hybrid child
Chrno crusade
Glass mask
Koe no katachi
You can watch these anime too:
Madoka Magica
Code geass R1+R2
Hybrid child (originally a manga but the feels you get watching the anime are REAL)
No 6
Byousoku 5 Centimeter
Kimi no Na wa.
Myself yourself
Ookami Kodomo no Ame to Yuki
Suki ni Naru Sono Shunkan wo.: Kokuhaku Jikkou Iinkai
Hotaru no Haka
I want the saddest manga you've read. I want to feel sad and cry to myself. It can be yaoi, shoujo, romance/josei, or shounen etc.