http://www.mangago.zone/read-manga/lonely_to_organdy/ (most manga by this author make me cry tbh xD)
http://www.mangago.zone/read-manga/bokutachi_futari_ga_koisuru_riyuu/
http://www.mangago.zone/read-manga/the_inheritance_of_aroma/
http://www.mangago.zone/read-manga/kosha_ura_no_natsu/
http://www.mangago.zone/read-manga/sorekara_kimi_wo_kangaeru/ (first chapter and last two pages of chapter 4 XD)
http://www.mangago.zone/read-manga/itou_san_kuraka_sui/
Get your tissue boxes ready?? (〒︿〒)
Oh there's also this one http://www.mangago.zone/read-manga/mahoroba_days/ don't remember why but it made me cry lol (´･_･`)
http://www.mangago.zone/read-manga/the_inheritance_of_aroma/ was the saddest one ╥﹏╥
Don't let the art put you off. This is just what you're looking for:
http://www.mangago.zone/read-manga/senya_ichiya_shitone_no_himegoto/
I recommand this too. Really great drama and character development, one of my favorite mangas.
http://www.mangago.zone/read-manga/koigokoro_wa_neko_o_mo_nurasu/ is another good one, though it didn't make me cry like the other one.
searching for a good, deep yaoi, like tragedy in the past or someones death... maybe one which made you cry before? ╥﹏╥