Iron Mal:
My personal favorite would have to be Samus Aran from Metroid. Simple reason really, she has one of the coolest suits of armor I've ever seen (short of Warhammer 40k Space Marines) and makes a living blowing stuff up. That and the fact that she useually goes around killing local wildlife (seems that she also has something against peta...I like that).

I also find it interesting that when it comes to the topic of sexism in gaming, people are very quick to deny Samus' femininity since she happens to be a strong female character (and protaganist, thats even rarer) who acts alone and litereally kicks ass under the pretense of her wearing full power armor throughout the game (that would undermine their arguement though, wouldn't it?).

Well-said.... Samus is definitely fantastic and downright cool. If she didn't have the ability to freeze enemies, though, I think she'd only be 75% as cool

Telekinesis:

Zero121090x:
My favorite has to be Tifa Lockhart from Final Fantasy. Why? A Couple Reaons:

1:She's Not A typical shallow, always-gets-captured-in-the-games-she-decides-to-show-up-in, character like Peach or Zelda.

Yes, she's the generic manly/brutal female instead.

She's not manly/brutal. She's tsundere. She's cold hearted and brutal to everyone except the person who she loves so huggy-muggy much. Eventually the power of the one she loves thaws her otherwise ice cold heart and she actually acts like a human being to other people.

Telekinesis:

Zero121090x:
My favorite has to be Tifa Lockhart from Final Fantasy. Why? A Couple Reaons:

1:She's Not A typical shallow, always-gets-captured-in-the-games-she-decides-to-show-up-in, character like Peach or Zelda.

Yes, she's the generic manly/brutal female instead.

Not really. :/ She is still extremely feminine. Not to mention the fact that throughout the entire freakin game (Final Fanatsy VII) she's trying to get Cloud Strife which was both sweet, but sometimes annoying.

Plus she's dead sexy which I sadly admitted. Dont believe me, check this out.
http://en.wikipedia.org/wiki/Tifa_Lockhart

HalfShadow:
Barring that, whichever ones keep their mouths shut.

The only vocal sounds Samus makes are pain/sex moans.

i have to say, i have a particular fondness for Ivy from SC. the motion physics of the 360 version... woah...

Sheik, from OoT. Loved a helping Zelda for once.

Take a wild guess.

Also, why is Wright's office filled with teenage girls? Seems kinda creepy/illegal to me.

Souplex:
Take a wild guess.

Also, why is Wright's office filled with teenage girls? Seems kinda creepy/illegal to me.

It's a Japanese game in an anime style. That's about all I need to say, I think.

Hm... female character... I like most of the female main characters in Final Fantasy VI. I could get into a whole thing about how they represent the classic roles that females play in their lifetime in an almost mythological way... but I won't. Suffice to say that none of them are too stereotypical in video game terms.

Tanya from Red Alert. She could kill people faster rocking the dual-pistols than 5 riflemen could with machine guns. Plus she carried enough C4 to level an entire city one building at a time.

Joanna Dark from Perfect Dark
Alyx Vance would be second, but thats only because shes not a red head like Joanna

Does it ever bother any of you that if these ladies were real they probably kick our asses before we could even say "Hi, my name is..". That may be the reason why I'm glad there just video game characters.

I'd say Alyx Vance for sure but let me throw out Lara Croft as well, I know as the games went on she mutated into some late 90's horror story but the first iteration (tomb raider 1 & 2) she had just the right amount of sass while the sequels just turned her into a bimbo. Compare the promo shots for Tomb Raider 1 where the focus is on her dual wielded Browning pistols to Tomb Raider 3 where the focus is on her plunging neckline.

Toby Gard who invented Lara Croft got kicked off the Tomb Raider team half way through TR2 as he continually objected to the hyper sexual representation of Lara as it was destroying her image. He was right, and after Core design when bankrupt after the 6th TR game, the American team who took over hired Tomb Gard right away and has been creative director from Legends onwards.

Chell from 'Portal' is by far the most compelling female character of any game.

I don't know if she counts though; I never figured out whether she was human or a cyborg/android.

Tifa Lockheart

Amnestic:

The reason I choose these two is because they aren't bad-ass action girls, which is annoying as fuck. Also, they're hot.

Wait. Wait. You say Yuna from FFX-2 because she ISN'T a bad-ass action girl?

Could I borrow your copy of the game? I think I played a different version. FFX-2 had Yuna ooze 'bad-ass' action girl as bad as Lara Croft. It was a little bit revolting at times.

Well, yeah, she was the main character and did some over the top action scenes, but if you remember, she was also sort of shy. She wasn't all like "yeah, we're gonna kick some ass! I'm gonna respond violently to the attention of every man because I'm a bad-ass, yeah!" But at the same time she wasn't a helpless, mindless moron like Zelda or Peach or every other female character who isn't a bad-ass action girl.
Besides, she's hot, and that's enough for me.

Alyx, Half-life 2.

Her expressions were so human, i actually cared about what happened to her. Not on like a realistic level, but she easily takes the cake.

Rayne from Bloodrayne.

Im gonna go with Rinoah Heartly

Man a Few
Ashley Williams from Mass Effect
Bastila from Knights of the Old Republic
Glados from Potal (female AI counts right?)
Chell from Portal, ya I know she doesnt talk

Thats gotta be it I guess

Either Alyx Vance, April Ryan or Zoe Castillo.

*points to avatar*

I know some of you are thinking, "But she's annoying as hell!" Give her time. You'll see why.

TheGreenManalishi:

HalfShadow:
Barring that, whichever ones keep their mouths shut.

The only vocal sounds Samus makes are pain/sex moans.

She talks in Brawl when she's in the Zero Suit, although she sounds a bit... well, you know.

I'm fond of any female character that doesn't have breasts larger then her face and isn't A. A panty dropping whore or B. A pyschotic sadistic evil ball crushing hoe-beast thats the poster child for militant feminism or C. A complete ditz or loony

So:

Bastila Chan - Knights of the Old Republic
Alyx Vance - Halflife 2
Jade - Beyond Good and Evil
Amatsaru - Okami YES I MEAN THE DOG
Lara Croft - Tomb Raider: Legend, and in none of her other games. Ever.
Ginchiyo Tachibana - Samurai Warriors 2

I don't recall the name of that one girl in Hot Coffee... :V

But, to be serious, Samus Aran. Definitely.

Nariko from Heavenly Sword and Meryl Silverburg from the MGS Series.

Jade from Beyond Good & Evil, hands down.

Alyx Vance is a close second, and following in third would be Lulu from FFX.

I'm going to have to go with Terra Branford from FFVI. Not your typical girly-girl, has a deep story, is arguably a standout character in the cast.

Terra and Samus are good ones as well. FFVI had a great cast of characters, including the most amusing thie- I mean, Treasure Hunter, ever.

because in the gamecube game super smash bros she has that awesome transformation she has the best attacks

I cant believe nobody has mentioned the chick (God, I cant even remember her name) from the original Far Cry. Crytek did an awful, half-assed job at making an attractive heroine for the player to lust for.
"Hmm, this scene calls for plot explanation. I better strip down to my bikini and wash myself here in this waterfall."

Although the voice acting was top notch; who could forget memorable lines such as:
"I'M GOING TO SHOOT YOU... IN THE FACE!"
"SUCK IT DOWN!"
"BITE MY ASS!"

Mmm, such were the days of 2004.

April Ryan (The Longest Journey) - The most down to earth and real female character ever, imo.
Shiki Misaki (The World Ends With You) - She's really cool, plus her backstory is pretty darn interesting.
Tifa Lockhart (Final Fantasy VII) - Tifa just oozes charm.
Rinoa Heartley (Final Fantasy VIII) - She's a very playful character and I found her charming.
Yukari Takeba (Persona 3) - Yukari felt very genuine to me, and her banter with Junpei is priceless.

Kos Mos from Xenosaga

Totally a broken record, being half my posts involve these names:
Bastila and Exile. Two hottest jedi's of the old order. Also two of the most deadly.

Mona sax or Mui from Mercenaries.

http://en.wikipedia.org/wiki/Bridget_(Guilty_Gear)

Bridget....... Oh wait.... Nevermind..... -goes in corner and questions masculinity-

But seriously,

http://wildarms.wikia.com/wiki/Image:Virginia_Maxwell.jpg

Virginia Maxwell gets my vote, she's a great character because she's extremely flawed, fails at everything for a while because she is childish, she then matures then actually becomes capable of doing things, says a few cheesy lines, shoots stuff with her pistols, then gets the crap beaten out of her by a demon, but that's besides the point. She's a well built character compared to most these days, even if a bit annoying in personality at times.

And the only reason I didn't vote for Alyx is to spite her, because in HL2E1, I hated having to push a car in the way of the ant lions to turn the cranks, while Alyx just shot at them pointlessly with her pistol, when I could've taken my gravity gun and juggled them while she opened the damn door, the only thing I hated in the game xD

And Chell is (most likely) a human, remember in Portal, GLaDOS says. "The regularly scheduled test chamber was not available." Which was most likely a lie, but she used it an excuse for turrets.
Edit:
http://farm1.static.flickr.com/184/375369763_38916afab3_o.jpg
I realized the wiki didn't have a picture of Bridget xD

juandonde:
Kefka (I don't care that he is not female he is my favorite dammit!)

I love you.

Alyx Vance from Half-Life 2

Not a big boobed clueless bimbo, has a personality that stands out, and I get very attached to her character while playing.

Thats whats so great about HL2 and its episodes as well, it succeeds at bringing me emotionally attached to all the characters more than any other video game i've ever played.