Well, that's a BIIG question for me :D. Ever since I started reading manga I've cried
a lot. All of them are shoujo(except one) since I usually prefer to watch the anime adaptations of the other genres than read them. Anyway, what I can remember are: (only small parts of each one made me cry)
Hana To Akuma
Zettai Kareshi (a little)
Tomodachi No Hanashi (I was touched by their friendship :D)
Shiawase Kissa Sanchoume
KareKano (a lot, complicated feelings, mixed with sadness XD)
Life (sadness, happiness)
And lastly, the one that made me cry the most, and a lot, is One Piece!! All kinds of crying XD
My memory failed me again..:S I'm sure there are many other mangas which made me cry much more than those(but not more than One Piece ofc..NOTHING made me cry more than One PIece did!)..I would've put them instead of those if I remembered them...