1. Domon Kasshu
People complain about the lack of storyline (coherent or otherwise) in G-Gundam. Sure its just a crazy interpretation of the Kung-Fu TV show with Giant Mechs, but Domon and Rain make the show worth more than that. If he's in a game..thats my main. No questions asked.
God knows what it's like in English though.
2. Big Boss
Don't get me wrong. I like Snake (oh geeze...thats sounds like innuendo...oh god there we go again) but Boss is, was and will be a much more interesting character. Snake is a puppet of the system, while Boss saw the strings and cut them. I'm sure Snake/Boss appears on many people's lists...but thats for a good reason.
3. Ragna the Bloodedge
you could say there are some similarities between Raggy and Domon..and no doubt there are. He's the tough as nails, soft hearted anime stereotype. However, like Domon he manages to rise above that by virtue of his journey during Blazblue. The cutscene where he goes apeshit on Terumi is priceless.
Another popular favourite. He's a badass mofo who looks like a bit of a girl.
The intro cutscene from the 3rd game alone puts him in the running for best character of all time.
Edit: Note the WHITE hair.
Almost forgotten, the LoK series was my bread and butter in the last two generations. I love those games, and of the two protagonists Raziel was always the far more compelling character. His tragedy was one of the greatest told in videogames
How can you not love Tao? She's completely innocent, irreverent and obsessed with food and fondling women's chests. She's the comic relief that's actually funny and she's just a whole bag of fun.
7. Jin Kisaragi
When you first meet Jin he comes across as an arsehole, then a psychotic arsehole, then a gay incest psychotic arsehole. Of all the BB characters he develops the most from what he was, to what he will become, and I really enjoyed that transition. Also that scene with Tsubaki was almost heartbreaking.
Ryu is great but he has waaay too much baggage as a ninja (ironic considering some of the other characters here). I like my Ninjas to be weapons of mass destruction. Hotsuma is pretty much that..but with a badass scarf. Please bring him back sega.
9. Terra Branford
My main for Dissida.
I'll say that I have yet to play VI but I'd certainly look into a remake.
Her character is pretty much the only interesting one in the whole of Dissida, and she's fun to play.
I LOVE Disgaea. Its something about the humour, madness and number obsession that sits well with my personal taste. Laharl was the first, and my personal favourite of the protagonists. Adell is boring as hell (hmm that rhymes) and Mao....wait, no Mao is awesome too.
I would put all of the guys from Resonance of Fate here..but I'm trying to limit myself.
Vash is...well...He's Vash the Stampede to be honest. Straight talking, sexist and has crazy dance moves. I found the player characters in RoF some of the best formed that I have seen in gaming so far. Its a great game, and you owe yourself to play it if RPGs with a twist are your thing.
12. Naoto Shirogane
No. Not Chie.
I totally don't understand the Chie love on this site. Sure Galactic punt is damn useful..but she's just annoying. Naoto is funny, intelligent and has a great...sense of style.
Sure she dresses up as a guy, but considering the line of work she's in and the sexist nature of Japan..you can't really blame her.
13. Kanji Tatsumi
Hands down the best character in P4, and possibly one of the best in gaming.
You could argue that both Naoto and Kanji aren't 'protagonists' per se...but they are controlled by the player and are instrumental in the plot.
Kanji's growth as a person throughout the game only serves to show that Atlus know what they're doing when it comes to character based games.
14. Gideon Wyeth
I'm among the very few people on the planet that REALLY enjoyed Advent Rising, and I think it's criminal that they cancelled the trilogy. I enjoyed my time with Gideon. He isn't the deepest character in the world, but they hardly had time to build a character for him in the 12hr gameplay that we got. Think of this entry as 'What might have been'
15. Kazuma Kiryu
Yakuza is like marmite. You either love it or hate it. Personally I think its one of the greatest series ever made. Kazuma's character shares many similarities to Anthony Corleone in the Godfather Trilogy. He wants to get out..but he keeps being drawn back in. A multifaceted character, Kazuma is among the best.
Got no body parts? Well just shove some swords and some guns in there instead. Dororo's protagonist makes Astroboy look like the wuss he is...just, don't stand too close after he's killed a fiend mkay?