You didn't say anything about having a blood relationship or not. So I am picking a few from my favs -
http://www.mangago.me/read-manga/not_equal/ (real father-son)
http://www.mangago.me/read-manga/sweet_vs_home/ (step-father)
http://www.mangago.me/read-manga/zion_no_koeda/ (Foster father)
http://www.mangago.me/read-manga/kusatta_rasen/ (real father-son)
http://www.mangago.me/read-manga/tatsu_no_otoshigo/ (adopted)
http://www.mangago.me/read-manga/sumanai_masumi_kun/ (father in law)
Yaoi manga with father and son relationship?