My favorite Yaoi is Koisuru Boukun
If you haven't seen koisuru Boukun, I highly recommend it. The sweet and kind Morinaga Tetsuhiro falls in love with the violent and homophobic Souichi Tatsumi. I love the relationship so much, how tatsumi slowly starts to express his love more and more. It will forever be my favorite.
Second place: Yokozawa takafumi no Baai: sekai ichi hatsukoi the movie. I love this one so much as well! In sekai ichi hatsukoi, Yokozawa seems like a jerk, but he gets a happy ending. It's so freaking cute!