Some are sadder than others:
- Complex (it makes me cry just thinking about it)
- New York New York
- Amayakana Toge (there's rape)
- Corsair (there's rape)
- Dear Myself
- Doushitemo Furetakunai
- G-Senjou no Neko (questionable consent, from what I recall)
- Hana no Miyako de
- Hanazono no Kioku
- Haru wo Daiteita (not an extremely sad manga, but there are some really tear jerking parts)
- Love Mode (same as former, sadness wise; there's rape)
- Ze (there's rape)
- The End of Youth
- Itou-san (there's rape)
- Kasa no Shita, Futari (there's rape)
- Sayonara, Itoshi My Friend
- Michiru Heya
- Neon Amber Sign
- Kowagaranaide, Soba ni Ite (I didn't cry, but I know people who did)
- Koujitsusei no Tobira
- Sabita Yoru demo Koi wa Sasayaku (there's rape)
- Renai Ruby no Tadashii Furikata (spin-off of the former)
- 500-nen no Itonami (breaks your heart from the get-go)
aaaand this one
http://www.mangago.me/read-manga/beautiful_days/
(=・ω・=)

Do you know any Yaoi or Shounen ai manga that can make you cry hard? Just in case, I wanna cry now but I can't. Help me please...