Hereby SPOILERS:
Caim from Drakengard. Looking at the guy from afar, you'd be tempted to think that he looks like just another JRPG pretty boy, but you couldn't be anymore wrong. He loses his voice due to his pact with the one creature he hates above all others: a dragon. And instead of initially being a guy who cherished those around him, he soon turns into a right psychopath who kills everything in a blind rage from knights, dragons and monsters to children and giant demon babies. His sister loved him too. A little
too much. And in the sequel, he kills everything. Old men, villagers, knights, he doesn't discriminate. Kill, kill, kill. Even the Grim Reaper. That's right, his blade strikes one character so hard in the sequel that he kills "Death" himself in the process. I'm not lying. What a bad ass.
Dycedarg Beolve from Final Fantasy Tactics.
Just a glorious villain all around, he is evil to the very core and I've yet to come across a villain more repulsive than this guy. You hate the guy's guts and as one YouTube comment put it: "Dycedarg was a sneaking, conniving, backstabbing, intriguing, lying, selfish, murderous, treacherous, patricidal, fraticidal douchebag. And he's a jerk and I don't like him." (I know, pooling comments from YouTube? Blasphemy. But it's true.)
Garcian Smith from killer7. Such a marketing ploy by Suda, since Harman Smith isn't actually the main character, it's Garcian. And Garcian's story sure is fascinating. His style is very reminiscent of Sumio Mondo, Edo Macalister even mentions this at one point and their design is similar too - they are running from their past which by the end of the game they have to confront and "Kill the Past" to set themselves free from the chains that bind them in their life. Won't spoil it, but the ending is rather mindblowing. I generally really like the cast of killer7, but Garcian is the most interesting.
Runners Up (And tbh, I like these people just as much as the "top 3"):
The Four Snake characters from Metal Gear. Raiden also. FOXHOUND too (heck, the entirety of the cast from MGS1 & MGS2).
Francis York Morgan. What a character development.
Ash Riot. I mean, just look at that name! How couldn't he awesome with a name like that. He is the reinforcements. Probably my favourite protag in a 3D RPG ever.
Ramza Beolve. This guy, man, this guy practically does everything in Ivalice. He's everywhere. Meets everyone and defeats every foe (and there hasn't been an RPG with a cast of villains this large, that I've ever come across). He saves the world of Ivalice more times than any other protag in that saga. The guy is a walking death machine. Oh, and he has great character development - goes from rich nobility to living in the shadow of his brothers/father to self-righteous bigot to finally becoming his father's son and being unstoppable;
Goemon. All four of the playables are awesome.
Demi-Fiend.
Sumio Mondo. Best Suda character next to Garcian. He names his car "Giggs" and his suitcase "Catherine". Fans of Deadly Premonition can probably see some resemblance here with his design, but Sumio came first and I like them both myself (as in these quirky detectives). His character development is vintage Suda and the guy is just really funny. Probably the funniest character I've seen in a video game, actually.
Okay, I'll stop there. Seriously though, top 3? Pffft, boring.
