Let me also add the caveat this only applies to characters in games I'm really familiar with so there's no Alyx Vance for example, because I never got into to Half Life 2. I also avoided characters who didn't originate in video games, are anthro, or who are robots/holograms/otherwise abiotic.
So, onto the list (some minor spoilers):
10. Lucca, Chrono Trigger:
Lucca is a genius inventor who carries a big gun, casts amazing fire attacks and is pretty much responsible for saving the world. (If not for Lucca's malfunctioning transporter Chrono and crew would have never known about Lavos) She pretty much constantly saves the party's ass by being the only one smart enough to figure out how to overcome the things they encounter that can't be simply beaten into submission. Lucca is kind of lacking in the stats department, but luckily her father makes a variety of special items that help compensate for that. I'd like to complain about her needing her daddy to fix her problems, but I feel confident that she could design her own armor if she wasn't so busy doing anything even remotely intellectual in the party. In spite of her weak base stats Lucca has some pretty powerful magic though, she is essential to both the strongest triple tech attacks in the game(Dark eternal and Omega Flare), the strongest double tech in he game (antipode 3) and her single tech, Flare, is the second strongest single tech in the game, so she's certainly not lacking attack power (unless it's a monster with magic resistance).
Unfortunately in spite of her awesome qualifications she also gets relegated to being your archetypical smart nerdy girl in many ways. Short Hair, Check. Baggy clothes, Check. Glasses, Check. Never the main love interest, Check. Being a glasses sporting female genius who isn't romantically interested in her childhood friend isn't necessarily a bad thing, it's just that it's so cliched and honestly Lucca deserves better than a sorry cliche. Though, in spite of being at least 70% walking cliche she still manages to be a pretty admirable character.
9. Carmen Sandiego, Where in the World/Time/Space is Carmen Sandiego:
8. Chun-Li, Street fighter Series:
Chun-Li is one of the first really recognizable token female characters. First appearing in Street fighter II in 1991 along with 7 male "world warriors" and was the first female playable character in a fighting game. In spite of being the token girl Chun-Li is consistently portrayed as being strong, muscular and capable of holding her own with the boys. In subsequent games she's been joined by a full roster of female fighters, but she's usually the only one who's fully dressed, as apparently for the "strongest woman in the world" the chain mail bikini principal does not apply. Sure there's a wealth of Chun-Li bikini figures endlessly flowing out of Japan and a few questionable alternative costumes so there's no denying she's sexy but she generally errs more on the side of badass. Chun-Li isn't just the first token girl though, she's a face of the game and often voted as the most popular characters in the entire franchise, beating out even Ryu and Ken. In her earliest incarnations she was a bit weaker than the rest of the roster, but over the years she's developed into one of the most solid and consistent fighters on the roster.
7. Sniper Wolf, Metal Gear Solid:
I have to note sniper wolf definitely has sex appeal built right into her character design, there's zero reason for her to be running around half unzipped in the snow other than gamers like boobies. But she's a lot more than a busty girl with a bug gun. She's a world class assassin supposedly able to wait days, even weeks for a target without moving or eating, while she doesn't have to wait that long for Snake and Meryl to wander out into the open, she proves what a single well placed shot can do to ruin your day. When Snake encounters her a second time, she proves that she's also a master of camouflage perfectly blending into to the snow field during your battle. All of the foxhound members that are part of the Shadow Moses uprising have interesting back stories, but Wolf's is a little more developed than most. She's not just a run of the mill super warrior Snake manages to best, she's a believable multi-facted person who just happens to be deadly.
6. Jill Valentine, Resident Evil 1:
Jill has evolved over the years to include a lot more T and A and have a lot less character development and depth, which is why I'm only citing the original game. In RE1 Jill's default outfit is pretty unflattering, not to the point where it makes her ugly, but it's pretty far from fan service. She also is one of the strongest members of her elite team of mercenaries, being one of a few that survives the excursion into the mansion. She also is one of the few female characters in the video game universe who can not only keep up with the boys, but she is much more useful than her male counterpart. Unlike Chris, she has a bigger inventory, plays piano and is the master of unlocking. She does fall victim damsel in distress syndrome a number of times requiring Barry to keep her from becoming a "Jill sandwich". However, because of Barry she doesn't have to carry around a bunch of useless items in limited inventory space unlike poor Chris, so it's kind of a positive in this case. In spite of needing the occasional saving, Jill is still a pretty kick ass character. She manages to mostly hold her own in mansion swarming with zombies, and defeats the nasty human civilization threatening bosses mostly unassisted.
5. Lara Croft Tomb Raider Series:
I have to point out that Lara is totally a sex symbol, she's been redesigned to be more "normal" now but she's still got an awful lot of T and a good amount of A bobbing across the screen. But being sexy doesn't mean you can't be a well developed interesting character and Lara actually does have a lot more going for her than her cup size. She's smart, strong and independent. Lara struts into ancient tombs all by herself, no silly local guides like the archaeologists use. She starts off armed with her wits, a pair of pistols and world class gymnastic skills. She has the strength to push aside those boulders blocking her entrance to the tomb, the intelligence to solve those insane puzzles ancient peoples seemed to litter their places of worship with, and the marksmanship to take out crazed creatures out for blood while she's doing it. Should she encounter someone in one of those tombs, Lara doesn't fall in love with them or take it as her cue to wait to be rescued, she usually tells them to get away from her artifacts and GTFO before she starts shooting.
Lara's changed a lot over the years and in her many incarnations, but in spite of being one of the most recognizable sex symbols in all of gaming, she's managed to stay smart, strong and competent.
4. Faris Scherwiz, Final Fantasy V:
Faris is a cross dressing, sword wielding, trash talking pirate captain. Her crew (and the party at first) believes she's male, but she's still so charismatic they fall in love with her anyway. You find out later in the game she's a long lost princess, but she chucks away her royal duties and dress at the first opportunity to go back to being a pirate. If that's not weird (but awesome) enough she also has the highest base stats of any character in the game, a feat which hasn't been seen since the most recent Final Fantasy game. So not only does she have a great character concept and while I'm at it, a pretty fabulous character design, she easily has the best black trench coat in an RPG this side of Sephiroth, but she is undeniably badass. That's not just an opinion there's cold hard numbers to back it up.
3. The Boss, Metal Gear 3: Snake Eater:
The Metal Gear series actually features a pretty large number of well developed capable and confident female characters, as it's a series that really excels in making fully developed wonderfully realized characters of any gender. The Boss though, has to be one of the most impressive. She influences the entire series, being the director mentor to big boss, and in turn the indirect mentor to solid snake and liquid snake. Not to mention her connection to Ocelot who is consistently causing problems for everyone. Though just being the Metal Gear equivalent of a King maker would be enough, but The Boss is pretty awe inspiring on her own terms. She's the head of the Cobra unit, which contains some of the most intimidating bosses in any of the Metal Gear Games, Co-Created CQC, saved the world from nuclear destruction, gave birth on the battlefield and made battling in a field of flowers completely badass. In spite of being a main antagonist and intimidating killing machines she's also likeable and you finish the game respecting the hell out of her. She also manages to be pretty and feminine (and not just when her sneaking suit is half zipped) in a slightly more mature and completely believable way. For the most part she embodies everything a well written strong female character should
2. Samus Aran, Metroid Series:
1. Heather Mason, Silent Hill 3:
Silent Hill is no place for anyone ever, let alone a young girl who hangs out at the mall in her free time, but Heather doesn't care. Unlike most of other protagonist in the series Heather doesn't go into the accursed town looking for ghost stories and giggles, Silent Hill comes to her full force. Instead of cowering in a corner and crying like any sensible person would do, she hesitates enough to be human, then picks up a gun and starts blowing away the nightmare fuel so she can make her way home. Arriving home with her world turned upside down, she doesn't take this opportunity to cry or breakdown or get someone to fix it for her. Instead, she vows revenge on the whole evil town and goes out to take care of business.
Heather is one of the most believable game characters of any gender. One of the few characters who when faced with insurmountable odds and a mind blowingly awful situation doesn't just spout manly one-liners, ask inane questions, or mindlessly stick her hands where no thinking person would. Heather basically tells you: Look, that nasty pile of bloody monster parts on the stretcher, yeah it's upsetting and I'm certainly not touching it, but I don't have time to be upset by it right now, get back to me later and I'm sure I'll have some words for it. Heather manages to be feminine in her sporty skirt and vest combo, without being distractingly sexy and manages to be strong without any of the sometimes grating (even for another woman) archetypical strong female character traits. Overall, Heather's gender is about as important as her shoe size. It's a part of her, but doesn't define her life or her character. That her gender is so gloriously unimportant, is one of the things that makes her one of the best portrayals of a woman in any video game ever.
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