the best ?
golden days ( the best manga i read so far )
life senjou no bokura ( 2nd best manga )
Not really as sad as the other suggestions but I wanted to follow and contribute.
http://www.mangago.me/read-manga/hana_no_miyako_de/
(Also, it's a standalone prequel, you can read the main story if you feel like reading something sweeter)
Oh, didn't notice it has been already suggested.
The ending of this is pretty sad, but the story overall is sweet so it might not be exactly what you're searching: http://www.mangago.me/read-manga/paradise_view/
Any tragic yaoi and really really sad plot? I'm in mood to cry