Sanctus91 said:
1.Raziel - Legacy of Kain
2.Geralt - The Witcher
3.Ezio Auditore - Assassin's Creed
4.Kain - Legacy of Kain
5.Arthas - Warcraft
6.Altair - Assassin's Creed
7.Garrus - Mass Effect
8.Haytham Kenway -Assassin's Creed 3
9.Lord Woolsack - Stronghold
10.Miranda - Mass Effect (10/10 looks

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Miranda on the 10th place? Why? Miranda sucks.
Halso, Haytham Kenway, although an awesome character, is not a protagonist, but an antagonist. Garrus isn't a protagonist either, but a side-character.
My top 10 protagonists:
1. Link (young version) - The Legend of Zelda series (technically not just 1 character but multiple)
2. Geralt of Rivia - The Witcher series
3. Adam Jensen - Deus Ex: Human Revolution
4. Ezio Auditore - Assassin's Creed II
5. Ethan Mars - Heavy Rain
6. Connor Kenway - Assassin's Creed III
7. Norman Jayden - Heavy Rain
8. JC Denton - Deus Ex
9. Altaïr Ibn-La'Ahad - Assassin's Creed
10. Lara Croft - Tomb Raider series
I probably have the strangest number 1 on my list ever. I'm willing to explain it, but it will be a longgggggggg post I think. I have to admit that my nostalgia and personal fandom for Zelda did play a role in my decision. I'm a bit of a Zelda fanboy, so my list of obviously biased. That doesn't mean I can't justify my decision to put Link on the first place though.