'Cause I'm a sucker for lists, that's why. Any nominations? Please don't say Lara Croft. In fact, I'll start the list with some obvious ones.
 
Lara Croft (Tomb Raider series)
Rayne (BloodRayne)
Samus Aran (Metroid series)

Lara Croft!
 
Now that I got that out of the way, I agree your list so far, but...and I have a few additions.
 
I'd include Alyx, the first lady of Half-Life. She represents to me why I like Valve. Alyx isn't a sex symbol, she's a strong lead character. I think it's testimant to their work on making characters real that I forgot there were a lot of women in Half-Life 2, many fighting right along with Gordon. Deus Ex was the same way, though I didn't like those women.
 
Another one that just came to mind is Aribeth from NWN. Actually, pretty much all Bioware games have great female characters. Bastilla from KOTOR; Silk Fox from Jade Empire; and let's not forget the other NPCs who'd join your party. I'm particularly fond of Mission Vao.
 
Here's a couple more:
Sarah Kerrigan (StarCraft)
Meryl Silverburgh (Metal Gear Solid)
Bella Goth (The Sims)

Kerrigan from StarCraft is the one I remember the best. She had a great NPC role as a human, then gets reborn as a Zerg - how cool is that?

Damn, beat me two it!
 
I can't stand Lara Croft in the video games, prob cause I can't stand those games!
 
Kerrigan (Starcraft/Starcraft Brood War)
Alyx Vance (Half Life 2)
Samus definitely!
B. Orchid (Killer Instinct/Killer Instinct II)
Anarki (Quake III - ok lol, I have no idea what i'm thinking)
The chicks from DoA (now i'm really losing it)
 
 
There seems to be so few good female characters....the first 3 are the best, Kerrigan being my fav, the character had soul, evil soul though    .

Etna from Disgaea
hmm...
Not sure if its because I'm just drawing a blank or because most female characters are pretty two dimensional but thats all I got for now.  I'll probably think of more later.

Disgaea, wow. Nice catch. A nice dark horse nomination for the list.
 
Thanks for the feedback. I'm up to about 50 characters so far. The list should be online in the next week or so.
 
And if you have any thoughts on who might play some of these characters in a movie, if they haven't already been adapted, throw those suggestions in as well.

Is this another article you're working on or are you just going to blast us with a huge edit to your OP?
 
I'll be thinking about those movie ideas over the weekend...

American McGee's Alice - Supposedly, is already being made into a movie starring Sarah Michelle Gellar.
 
Ms. Pac Man - Could star Tyne Daly or Roseanne Barr.

 
Already got that one on the list, but thanks. And it's true, Buffy is playing Alice. Couldn't think of a better casting choice myself -- which is hard, by the way. I mean, after all, who could play Sarah Kerrigan in a movie?

April Ryan from The Longest Journey.
 
Hands down.  No objections even possible.  I will personally track down & silence anyone who so much as suggests it's even possible for another character in a game to top her.
 
 
From there, I tend to like SHODAN from System Shock 2, Victoria from Tribes Vengeance, that mutant chick from Tiberian Sun (yes, I'm kidding), Farah from Prince of Persia: Sands of Time, and I'm having trouble thinking of any more serious contenders right now...

 
Wow. And I though I was a big April fan. I totally agree with you Gyro. I just started playing The Longest Journey, and she easily won me over.
 
Now the question is, who'd play her in "The Longest Journey" movie?

April Ryan is indeed a great female character

What about the main character from the NOLF games? (Can't recall the name unfortunately).

Cate Archer - excellent choice Llamaman! She was great, and I can't believe I didn't include her in my 1st post...

How great were those games?  (/awaits NOLF3 with little hope]

 
Little hope indeed - and that is a darn shame. The second one in particular was a game I have replayed more than almost any other - good sneaking, quirky story and characters, two thumbs WAY up!

Okay, so who plays Cate Archer in the movie?
 
Kate Beckinsale? Kate Winslet? Rachel Weisz? Posh Spice?

 
I vote for Mila Kunis - need to see her do something besides comedy.

 
Beckinsale would be nice, and she has the requisite wardrobe from the Underworld movies. Rachel Weisz would be excellent as well - very easy on the eyes and ears. Winslet is not sufficiently winsome - hard to imagine her slinking around in Pleather convincingly. Posh hasn't enough neurons to rub together, and Ms. Archer is a bright girl, so Posh is out altogether. No other ideas coming at present, but I'll add some as they occur...

Anyone remember the Nazi Assassin babes in Return to Castle Wolfenstein? No, not their fat overmaster, the girls themselves.
 
Anyone recall Crystal Steele from Blade Runner?

 
I remember they were used a lot for screenshots in game magazines.
 
Speaking of assassin babes, I can't believe I forgot about the ninja chicks in the original Half-Life. Now those were scary.
 
Oh yes, Princess Daphne from Dragon's Lair.