Kazami Yuuji (Grisaia) : Well, this is the pretty much mandatory in every list for best protagonist for me
Rance : Even though I'm not fond with guy from earlier part of the series but this guy is freaking badass in Rance 9 and 10
Ushiromiya Battler : It's freaking Battler
Celica Sylphil from Ikusa Megami series : Watching this man development from Ikusa Megami Zero and Verita is really something else.
Niimi Kakeru from 9 nine : I like this guy. This guy remind me of Kadakora Kou from Baldr Sky but with more reserved feeling.His conversation with his sister Sora (best brocon),makes this guy easier to relate and connect.