1. LIGHTNING - FFXIII (Gets five points)
2. Hope - FFXIII
3. Vanille - FFXIII
4. Fang - FFXIII
5. Sazh - FFXIII

I only played FFXIII.

1. Auron (FFX): He is BA, has nice character development.
2. Squall (FFVIII): Has massive character development, and generally also has BA moments.
3. Kimahri (FFX): Had very little to say, but was still BA. I also liked his spear usage.
4. Balthier (FFXII): Also BA, to me he was the main character of FFXII
5. Seymour (FFX): Was a fun villain, and had his quirks

1) Cloud FF7.
2) Rinoa FF8.
3) Zidane FF9.
4) Squall FF8.
5) Terra FF6.

1) Lightning FFXIII
2) Yuna FF X
3) Tidus FF X
4) Balthier FF XII
5) Vanille FFXIII

Limited to 5 character means it is hard choices, FF9 has enough alone to fill any list.

1) Vivi FF9 - He's awesome
2) Fran FF12 - I'm sure I mainly played the game because of her, never play it without her being in my main party.
3) Rude & Reno FF7 (only from FF7) - As a unit/team. They were funny, the fact they were generic villains yet had personalities. Rude wanted some Tifa action...
4) Squall FF8 - His development in the game was both pushed upon him yet also forced by his own stubborness.
5) Red XIII FF7 - A talking cat people.

Honourable mention to Fang from FFXIII, the game is the worst FF game I've played, it has awful character except her. Who is a powerful female character who doesn't take any crap and just wants the girl. didn't make the list because she' in FFXIII.

You know what? I wasn't actually going to vote myself, other than that sample at the front, but here's my Top 5. Note that I haven't played every single game, but considering how some people on this thread have admitted to only playing a single game, I think I'm qualified enough.

P.S. Spoilers Ahead!

1. Auron (Final Fantasy X) - Has everything I want in a character of his archetype. Despite being not that old, he is definately the wise old mentor, and a badass one at that. He has a rich backstory, a compelling character arc, and a big sword. Plus, from a gameplay point of view, he's one of the more useful characters, being the best physical attacker in the game thanks to his piercing ability and high attack power, which only reinforces the idea of him being a badass. Oh, and his character theme is cool. Not much to say about him, but I really think that Auron is a great character in every major respect. And from the looks of it, a lot of people agree with me.
2. Rydia (Final Fantasy IV) - My favorite female character in the series, she's if anything even more of a badass than Auron. She's introduced via the tragic slughtering of most of her village, including her mother, by the unwitting Cecil and Kain. At the time, she's seven years old. So, what does she do when her mother's murderers come up to her? She summons a Titan with an attack so powerful that she CHANGES THE GEOGRAPHY OF THE WORLD MAP. I'm sorry for the bold caps lock, but permaently changing the world map is something usually reserved for major villains with godlike powers or dwarves with dynamite, not 7-year-old girls. Anyway, this alone would have made her noteworthy, but the rest of the game features her as a major character. She grows and matures at a fairly quick but believable pace, is the center of some good plot points... and then she gets swallowed by the giant Leviathan. Oh well, that was... wait, in a plot twist that's actually decent, she doesn't die. Instead, she was brought to an alternate dimension where Summons come from, where she spends a decade (about two weeks in the outside world) training her behind off. Then, when the big bad guy has the heroes on the ropes, she comes out of nowhere mid-boss-fight and saves the day, armed with a variety of new abilities that make her the best offensive mage in the game. Throw in some romantic tension with a Ninja latter on and being one of the two non-Baron characters to face the Final Boss, and you have the original awesome female character in the series, as well as one of the finest. Seriously, the only reason she's not #1 is the story-telling limitations of the early SNES era.
3. Balthier (Final Fantasy XII) - Rather than being a badass character, Balthier is "cool" and "savvy." That's almost as good. Final Fantasy XII should have starred him as the main character, thrown away Vaan and Penello, and made all four remaining characters playable at once. Not that Vaan and Penello were terrible, just that even as an angsty teen, I thought they just seemed to be thrown in to appeal to the angsty teens. Anyway, Balthier gets a lot of points for being a sky pirate, one of the better occuations ever conceived. His character design resembles both that of a traditional pirate and a JRPG/anime character, making him look the part for everything he is. He's sharp and cunning, but has quite the ego, calling himself "the leading man." Which he should have been, so fair's fair. He's also got a nice backstory, but the reason I like Balthier is what he is in the present: a genuinely cool JRPG character, both by my teenage and current stadards. The main thing holding him back for me is his actual gameplay. Maybe Balthier is actually a great character if you know what you're doing, but I found him to lack the physical or magical attack power to be very useful. Sure, he was fast, but he was not fast enough to be very handy in combat. Unfortuantely, I feel that Vaan, for some reason, was the best character in combat in FF12, for some reason.
4. Tidus (Final Fantasy X) - Tidus is not a cool or badass character. He's a whiny teenage jock who got in over his head. So naturally, I should hate him. But for some reason, Tidus is one of my favorites. Why? Well, partially because he's one of the more sympathetic main characters in the series. Unlike the badass trained military personal of some other games, this guy is a pampered yet moral athlete who sees his world get destroyed in a single night. He's a reinterpretation of the bumbling idiot hero, one who has no idea what this strange new world of Spira is like, but is constantly doing his best to do the right thing. And sometimes, he ends up being a bit insightful. Ultimately, his romantic relationship with Yuna is not necessarily the best in series history, but is possibly the most tragic throughout. Tidus is the closest thing the game has to a player stand-in, and =does this job well, but he is his own man. Add some family issues, tie in some character development with other cast members, and make him a genuinely useful and interesting character to use in battle, and you have my favorite Final Fantasy protagonist whose actually relatable to me. Even though he likes extreme water polo for some reason.
5. Babus Swain (Final Fantasy Tactics Advance) - Tactics Advance is not the least popular Final Fantasy game, but its story is often overlooked for being simpler than the original Tactics. With good reason, but the game does have some interesting characters to share. Chief among them, IMO, is Babus Swain. The only non-human character on this list, Babus starts out as Prince Mewt's right hand mage, doing anything necessary to protect him. And this is what he does throughout the game. He alternatively opposes and supports the hero and the game's various characters and factions whenever necessary to serve the boy he cares deeply about. This is a very interesting dynamic for a series aimed for teens. It's a story about an adult doing his best to help a child he loves. And despite not being THAT powerful, he's willing to fight the protagonist Marche, evil super-powered dark sides, and even go against Mewt's wishes, sometimes singlehandhedl, in order to help him. In his mind, his life is worth nothing compared to the boy he swore to protect. And I respect that. As a bonus, his actual abilities as acombatant are interesting.

Honorable Mentions: Kefka, my favorite villain in the series, and Minwu, the first really great character in the series.

Vivi (ffIX)

 Rikku (FFX)

Garnet AKA Dagger (FFIX)

Auron (FFX)

Paine (FFX-2)

I'm sorry, you'll have to pick only five or less. I can't split votes, because then that gives people different voting power by voting for over 5 characters.

Fixed.