is it bad when the first thing I thought when I saw the title was 'Is this the third one? Is it? IS IT??!!'

..cause that's what I was thinking..

ANYWAY

I nominate Link, from LoZ, and Pit from Kid Icarus while for Villains I'll toss out Ganondorf (LoZ) as well as... uh..

...Wario? yeah sure Wario (Super Mario/Wario)

Zakaro

I will nominate Sephiroth (Final Fantasy 7) and Albert Wesker (Resident Evil 5) for  the Villians

I will nominate Angeal Hewley (FF7: Crisis Core) and Samus Aran (Metroid) for the Heroes

Heroes: I Bravely Second Agnes and also nominate Bartz Klauser (Final Fantasy V)

Villains: I nominate Cyrus (Pokemon) and Gemini (Mega Man Star Force)

I nominate Lucas from Mother 3, and Samus from Metroid (x2).

Villains, I nominate Ridley from Metroid and...uh...

Black Shadow from F-Zero.

I nominate Ness from Motherbound and second Link from LoZ.

Also Majora from Majora's Mask and Ghirahim from Skyward Sword.

Second Samus, nominate Richard Conway (Gunpoint)

Second Ridley, nominate Spider (LIMBO)

Nominate Pit (Kid Icarus) and a Second For Samus

Hm... Villains... 

Comstock (Bioshock Infinite) Wallace Breen (Half Life 2) (I don't even know, I can't think of anything at the moment.)

Nominate Zero (Mega Man X) and second Pit.

Nominate Queen Sectonia (Kirby) and if it counts, Viridi (Kid Icarus). =P

Viridi wasn't a villain, was she?

Nominate Robin (Fire Emblem) and second Pit (Kid Icarus) for heroes.

Nominate Grima (Fire Emblem) and Ghetsis (Pokémon) for villains

Nominate Captain Falcon (F-Zero) and second Lucas

Nominate Sirius(Bomberman 64) and second Black Shadow

I'm not really sure I would put any GTA protagonist down as a "hero". As a protagonist? Definitely. But as a hero? Well... that's a lot of drugs and murder for a hero to be committing. 

How many people did Agnes's party kill though

I would put CJ down as the most morally right protagonist in the series. CJ is depicted as having a considerably less violent personality, occasionally giving his victims a chance to redeem themselves.

Changed since X cried about it.

And changed villain once more to show some Bomberman love

Nominate Zero (Mega Man X) and second Pit.

 

Nominate Queen Sectonia (Kirby) and if it counts, Viridi (Kid Icarus). =P

She antagonized Pit. Hmm.......

Okay then, what about Vile from Mega Man X?

He'll work.

Nominating/Second:

Link (Legend of Zelda Series

Professor Layton (Professor Layton series)

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Don Paulo (Professor Layton series)

Master Hand (Super Smash Bros. series)

Nominate Liang(Waking Mars) and Dust(Dust: An Elysian Tale) for the heroes.

Nominate the Medic(TF2) and the Gentleman (Monaco) for the villains.

~Unit#phntk#1

I feel like the main cast of TF2 would fall closer to protagonist, due to the whole MvM thing

Nominating:

Samanosuke (Onimusha Warlords), Starkiller (The Force Unleashed)

Ganondorf (Legend of Zelda), Malice Borg (Dark709's Comics: The Game)

I have nothing to lose, so I might as well do this, honestly. I'm also aware of the questionable first choice for the villains, but hopefully this works well enough.

Hero Nominations: John Marston (Red Dead Redemption), Gordon Freeman (Half-Life Series)

Villain Nominations: Big Boss (Metal Gear Series), and seconding GLaDOS (Portal)

Hero Nominations: Seconding Mega Man (Mega Man Series), E-123 Omega (Sonic the Hedgehog Series)

Villain Nominations: Seconding GLaDOS (Portal Series), Metal Sonic (Sonic the Hedgehog Series)

(Wow, all my nominations are robots.)

I feel like the main cast of TF2 would fall closer to protagonist, due to the whole MvM thing

Yeah, but protagonist =/= hero.

~Unit#phntk#1

Sorry, I meant Hero. Ugh, now I'm mixing up terms. >.<

Heroes: nominate Master Chief (Halo) and second Starkiller (The Force Unleashed).  

Villains: nominate Darth Malak (Knights of the Old Republic) and Kane (Command and Conquer).