1. Captain Malcolm "Mal" Reynolds
Nathan Fillion created one of the best leading roles in a Sci-Fi series with this part. Had the show been able to continue it would likely have given him a position amongst the greats like Picard, Kirk and The Doctor.
Mal ticks all of the required boxes for a protagonist: he is flawed, brave, heroic, funny and is willing to go to great lengths for those he cares about. In the dark and violent future given to us by Firefly, Mal does his best to stay moral but understands the limitations that one person can have, and knows when to betray his morality for the right reasons.
Further than just being a complex character, Mal was hilarious, as his dark sense of humour and frequent misreading's of situations caused him to come across as quick-witted yet clumsy at the same time. He backed all of this humour up, however, with extraordinary fighting skills and a threatening attitude.
The humour, the coolness and the heart of the show are all present in this performance. Therefore the Captain of Serenity is easily the best role in the show, as he's the most identifiable, and captures everything that made Firefly great, all in one character.