First place by far:
Colette Brunel
(Tales of Symphonia, Namco, GC/PS2)
Why:
1) She has alternate outfits, which is almost a guaranteed qualifier for honorable mentions if nothing else.
2) She blends about four different stereotypes that aren't supposed to go together. The angel shouldn't be the clutz, the angel shouldn't be the thief, the angel shouldn't be the prophet who understands everybody at first glance, the clutz shouldn't be the thief, the clutz shouldn't be the prophet, and the thief shouldn't be the prophet. It all makes absolutely zero sense, which is why it's so great, and why she ends up being such a well-developed character storyline-wise in a game where everyone else--except for Presea and maybe Zelos--is pretty shallow.
3) She saves the group multiple times by tripping and falling and it's insanely adorable every time it happens.
4) She's one of the most fun support characters ever. Normally I can't stand it when AI-controlled characters are backing me up, whether in Secret of Mana or Star Ocean 2, but Colette as an AI player tends to stun the enemy a lot without ever killing it and taking my glory.
5) Her theme owns my world.
6) She gets captured two or three times. Granted, they never actually show her tied up--if it did, that would probably etch her the
permanent #1 favorite character spot--but just knowing that it's theoretically happening is enough.
7) I think she's cute, regardless of what the haters think.
8) I like her English voice actress, also regardless of what the haters think.
9) I have absolutely no clue what the shoulder things hanging off of the sides of and over her dress are called, and that makes me happy.
10) I've never cried for a video game character before, but cried for her three times in the course of my first playthrough--then did it again on two of those scenes the second time through.
Second place by far:
Jigglypuff
(Pokemon series, Nintendo/GameFreak, GB/GBC/GBA/DS/N64/GC...
...and Super Smash Bros series, Nintendo, N64/GC)
Why:
1) The nostalgia factor of R/B/Y days, back when I thought Sing was a broken move because it put enemies to sleep with what really seemed like a lot more than 55% accuracy.
2) My current online name spawned from a shortening of "Jigglypuff."
3) She's simply by far my favorite character to play as in SSBM. Part of that is because nobody I play against knows how to use her, so they also don't know how to counter her (whereas other friends' specialties include Peach, Fox, Sheik, etc., all of whom I know how to deal with), but more of it is just due to insane aerial maneuverability. She's way, way too fun to play for me to rank her any lower.
Third place by far:
Rena Lanford
(Star Ocean: The Second Story, Enix/Tri-Ace, PSX)
(Star Ocean: Blue Sphere, Enix/Tri-Ace, GBC)
Why:
1) Not technically alternate outfits since they're in different places, but she has one outfit in Star Ocean 2 proper, another in the Japan-only Star Ocean: Blue Sphere, and another in the Star Ocean 2 anime (shown up above), and I really love all three. The only gripes I have with each is that the shoes of the SO2 artwork don't make sense for a girl who likes exploring and running around, ditto for the skirt of the SOBS artwork (although it really does look great on her and helps the futuristic look), and the anime artwork ditches the high socks while also making her look anorexic.
2) She only gets captured once, unlike Colette--but also unlike Colette, they actually show it. WOOO.
3) Like everybody else in Star Ocean, she's got an insane plethora of skills at her disposal. She fights, she has healing powers, she makes her own weapons, she makes her own armor, she makes her own accessories, she forages for survival, she sends birds to get supplies for her, she cooks five-star meals with only a few ingredients, she summons gigantic bunnies to transport her around, she plays musical instruments, she writes best-selling romance novels, and more, all at the age of 17. Crazy.
4) She's in a game the likes of FF6 and CT, where I keep and/or will keep wanting it re-released on a portable system until it actually happens.
Honorable mentions, in alphabetical order by game since I'm too lazy to figure out exactly where to rank them:
Sami (Advance Wars series, Nintendo/Intelligent Systems, GBA/DS) - Has very different abilities from all the firepower bonus COs in the series, a neat character design art-wise, and a theme so awesome it could probably be the main theme of the entire series.
Marle (Chrono Trigger, Squaresoft, SNES)
Kasumi (Dead or Alive series, Team Ninja, Dreamcast/PS2/XB/X360) - Like I said, alternate outfits will get any halfway decent female character into the honorable mentions. A fun character to play as, too.
Celes Chere (Final Fantasy VI, Squaresoft, SNES) - Good storyline, fantastic theme, and cute sprite.
Terra Branford (Final Fantasy VI, Squaresoft, SNES) - See Celes, except subtract the "cute sprite" part.
Tifa (Final Fantasy VII, Squaresoft, PSX) - Her art design really betrays the writing behind her, because she's a good "girl next door" type. Lacks a good theme, too.
Lyn (Fire Emblem 7, Nintendo/Intelligent Systems, GBA) - Has very different abilities from basically every other Lord in the series, a neat character design art-wise, and a theme so awesome it could probably be the main theme of the entire series. Basically the Sami of FE, to me.
Mist (Fire Emblem 9, Nintendo/Intelligent Systems, GC) - Just because there's something funky about a girl who starts off as a ground-based healer with 5 movement and turns into a mounted sword user healer with 8 movement.
Cassandra (Soul Calibur 2-3, Namco, GC/PS2/X-Box) - 236B and the valkyrie outfit do the trick. If PS2 dropped to $100 new and came bundled with something good, I'd really consider buying one just to play as Cassandra with new outfits.
Would have made the list or honorable mentions if they were main characters:
Schala (Chrono Trigger, Squaresoft, SNES)
Agrias (Final Fantasy Tactics, Squaresoft, PSX)
Beatrix (Final Fantasy IX, Squaresoft, PSX)
Eiko (Final Fantasy IX, Squaresoft, PSX)
Relm Arrowny (Final Fantasy VI, Squaresoft, SNES)
Yuffie (Final Fantasy VII, Squaresoft, PSX)
Rikku (Final Fantasy X/2, Square-Enix, PS2)
Tana (Fire Emblem 8, Nintendo/Intelligent Systems, GBA)
Marin (The Legend of Zelda: Link's Awakening/DX, Nintendo, GB/GBC)
Lemina (Lunar 2: Eternal Blue, GameArts/WorkingDesigns, PSX)
Precis Neumann (Star Ocean: The Second Story, Enix/Tri-Ace, PSX)
Had the potential to make the list or honorable mentions if they were human:
Kazooie (Banjo-Kazooie/Tooie, Rare, N64)
Dixie Kong (Donkey Kong Country 2-3, Rare/Nintendo, SNES/GBA)
Had the potential to make the list or honorable mentions if they showed personality instead of just cool abilities:
Alena (Dragon Warrior IV, Enix, NES)
Paula (Earthbound, Nintendo, SNES)
Porom (Final Fantasy IV, Squaresoft, SNES)
Rosa (Final Fantasy IV, Squaresoft, SNES)
Selan (Lufia II: Rise of the Sinistrals, Natsume, SNES)
Samus (Metroid series, Nintendo, NES/GB/SNES/GBA/GC)
The Girl (Secret of Mana, Squaresoft, SNES)
Lenneth Valkyrie (Valkyrie Profile, Enix/Tri-Ace, PSX)