Any mangas that in the beginning the seme rapes the uke but they end up together in the en...

Off the top of my head:
http://www.mangago.zone/read-manga/if_you_hate_me_that_much/

http://www.mangago.zone/read-manga/unbalance_na_netsu/

probably my favorites

Not sure i dont really know any on the top of mea head sorry :(

The most popular yaoi
http://www.mangago.zone/read-manga/you_re_my_loveprize_in_viewfinder/

http://www.mangago.zone/home/mangalist/119844/ this could help. look for yaoi rape in description

http://www.mangago.zone/home/mangalist/102039/

http://www.mangago.zone/read-manga/hidoku_shinaide/
This is one of the best yaoi mangas I have ever read ( ^ω^ )