
Where the father dies and then somebody moves in and plays the role of the father and the child falls in love with him and child is not young he is maybe 16 and looks manly

Maybe this one? http://www.mangago.zone/read-manga/bokura_no_negai/

I search for yaoi mangas where best friends become a couple but at the beginning that is just a one side love

XD well with your specificacions let me tell you about 3000 mangas like that XD

Here are some random titles:
http://www.mangago.zone/read-manga/rift_conro/
http://www.mangago.zone/read-manga/liquor_cigarette/
http://www.mangago.zone/read-manga/hitorijime_no_jouken/
http://www.mangago.zone/read-manga/mahoroba_days/
http://www.mangago.zone/read-manga/koisuru_taka_wa_tsume_o_kakusu/
http://www.mangago.zone/read-manga/toshigoro_no_otokonoko_to_are/
http://www.mangago.zone/read-manga/orutana/
http://www.mangago.zone/read-manga/koi_o_hitokuchi/
http://www.mangago.zone/read-manga/hima_na_no_de_hajimete_mimasu/
http://www.mangago.zone/read-manga/itsuka_tomodachi_ja_nakunaru_to_shite_mo/
http://www.mangago.zone/read-manga/jibun_katte/
http://www.mangago.zone/read-manga/yakozen/
http://www.mangago.zone/read-manga/soredemo_yasashii_koi_o_suru/
http://www.mangago.zone/read-manga/bokurani_matsuwaru_etc/
http://www.mangago.zone/read-manga/by_my_side/
http://www.mangago.zone/read-manga/waraibanashi_no_you_da/
http://www.mangago.zone/read-manga/tsuioku/
http://www.mangago.zone/read-manga/itoshi_no_nekokke/
http://www.mangago.zone/read-manga/boku_ni_datte_iibun_ga_aru/
http://www.mangago.zone/read-manga/saburina/
But anyway, ALL from the #close friends or #childhood friends tags fit your description. As anon said, 3000 mangas isn't exaggerated.

I search a yaoi where 2 students become lover but at the beginning they hated each other

http://www.mangago.zone/read-manga/a_man_like_you/
You probably already read this but

maybe search my tags for rivals
http://www.mangago.zone/people/tag/170865/rival/

I Search a yaoi in that Manga there is a popular and a unpopular guy and the unpopular guy is a Otaku but at the end or in the mid he become super popular and smart and he is in Love with the other guy they were also in school and the girls love the popular guy and hate the otaku (nerd) and as they see that he is pretty headsome they all want him hopefully you know what I mean ٩(๑❛ᴗ❛๑)۶

I'm not sure if he's an otaku but is a unsociable nerd
http://www.mangago.zone/read-manga/violence_na_kimi_ga_suki/
Hey i search for an yaoi where one guy is in love with a hot guy and the hot guy hates gay or dislikes them but in the end they come together. Hopefully you get what kind of yaoi I mean (▰˘◡˘▰)
I have not read it but i did read the last chapter. I think this might be one you would like?
http://www.mangago.zone/read-manga/sore_o_koigokoro_to_yobu_no_nara/