Best - tie between Zidane and Ramza. I liked Zidane as he was a charismatic good guy, one of the protagonists I liked. As for Ramza, a hero who fought for his idea even though history wrote as a heretic.
Worst - Vaan as he really doesn't drive the story cept for delivering a sword. To be honest I would rather have seen a Reks storyline than Vaan.
"Men in battle, do not need women. My love is my Sword!" - The Almighty Dekar from Lufia II
My favorite protagonist is Zack from CC: FFVII. He's got a great personality, he's built tough, and he has a really cool character design. He really needs to be featured in a better game as the main character, as I wasn't crazy about Crisis Core. My runner up was Cecil from FFIV.
My most disliked... now this is a tough one. I think I'd have to go with Lightning, she's just very boring to me (much like how I felt about FFXIII as a whole). I would've liked to say Vaan from FFXII, but unfortunately I couldn't bear through enough of the game to validate that choice, compared to how much time I spent on XIII.
1 Cloud (FF7 is and always will be the best) 2 Ramza (Tactics easily has the best/most adult themed storyline) 3 Cecil (Unlike most FF protagonists, he is not really whiny, just heads through everything) 4 Squall (Having a rival that wasn't majorly overpowered really helped humanize him) 5 Zack (I was surprised how good his character is, but he is only a side story) 6 Zidane (Being a thief archetype hurts him as a main, but at least a decent character) 7 Firion (Same idea as Bartz really) 8 Bartz (While the job system is cool it lacks to give Bartz any real long run impact) 9 Ceodore (Ends up being kind of second fiddle to his father) 10 Tidus (He's a decent character but really whiny, even by FF standards) 11 Lightning (I just didn't really like FF13 at all) 12 Terra (I don't consider her much of a protagonist as your never forced to use her) 13 Vaan (Same reason as Terra, but also an awful character) 14 Vincent (He's a cool character, but a terrible protagonist) 15 Luneth (Admittedly i'm not too familiar with FF3) 16 Yuna (X-2 was just a terrible game all around)