i’m going a diffrent route here.
kathy (don’t call me kathy) mallory from carol o’connell’s series.
the sisters, mouse and sister from ann george’s series.
ginger barnes from the main line murder series.
Daenerys was a good character I guess, but since I’ve only read the first book she doesn’t seem to be too great I think I like Arya so much better, now that girl had spunk.
Kitty
I don’t know about that. My own choice comes from the pages of Stephen King–Rosie McClendon from “Rose Madder.” I was so taken by that character as well as by the novel as a whole that I wrote a song about it (“Lady Rose,” included on my band Katzi’s final album “Pull.”) It’s a great novel, definitely one of my favorites.
I like the character in “There’s Something About Mary”.
That’s my kind of heroine (anti-heroine?)
Molly Kolodtny from William Gibson’s Neuromancer trilogy.
Chia Pet McKenzie from William Gibson’s Idoru.
Sonya Blue, from the Nancy Collins vampire books.
Genevieve Dieudonne from Kim Newman’s Anno Dracula.
The wife of Casubon in Middlemarch.
The woman professor in the movie House of Games.
Zenster –
First one’s Dorothea Brooke; don’t know about the second, but I’m sure somebody will.
My pick: Elizabeth Bennett
Astrid from White Oleander.
Dr. Margaret Ford as played by Lindsay Crouse.
Having been reading everything I can by Octavia Butler lately, my current favorite is Lauren Oya Olamina, from The Parable of the Sower and The parable of the Talents
magdaline
I doubly support this one, she was one coool customer. To bad P.C. Hodgell got screwed so badly by her publisher. I wanted more of that series, now I can’t even get the first two books. (My old library had them, and then some A**hole stole them, grrrrrrrr.)
Define heroine.
oh well, I’ll go with my own.
Dolores Haze
Rosalind from As You Like It
Nichola Six from London Feilds
Katherine Howard from The Fifth Queen
Since there seem to be a lot of science fiction: Trillian from, well mostly from Life,the Universe and Everything, where she saves all three from total distruction.
My favourite heroines are in Iain Banks novels -
The Doctor in “Inversion”
Sharrow in “Against a Dark Background”
Angela in “The Bridge”.
All very strong women who can be vulnerable at the same time. Smart, calm under pressure and not afraid to make difficult choices. I wanna be like that when I grow up!
I always think that his books would make great films if done properly, someone is going to make “The Bridge” and I don’t know if I want to see it or not. It would destroy the images of the characters and locations in my mind like “the Beach” which completely ruined the book for me. Also I would hate for someone to mess around with the plots because it made “better” drama.
Cordelia Naismith from Louis McMaster’s “Vorkosigan” series
Damnit, Lois, not Louis.
I’ve always been partial to Mara Jade in the numerous Star Wars novels. Also found Belindi Kalenda (a much lesser-used character) to be intriguing.
[shameless plug]
But, of course, my favorite heroines are the ones that I devlop on my own… feel free to check out some of the stories on my website to get a better idea.
[/shameless plug]
Mara jade is the BEST star wars female character!! 
Christa Cruitaire from Gael Baudino’s novel “Gossamer Axe”
Nova Kane from the old E-Man comic
Leiko Wu from the old Master of Kung Fu comic
Penelope and Circe from The Odyssey
Effie from “The Maltese Falcon”
Kinsey Milhone
Sand Saref and Silk Satin from “The Spirit”
Cordelia Gray from P.D. James’ novels “An Unsuitable Job for a Woman” and “The Skull Beneath the Skin”
Elizabeth Bennett from Jane Austin’s “Pride and Prejudice”
Two Doc Savage heroines: Hannah the Pirate “Mystery on Happy Bones” and Toni Lash from “The Devil Genghis”
Christa Cruitaire from Gael Baudino’s novel “Gossamer Axe”
Nova Kane from the old E-Man comic
Leiko Wu from the old Master of Kung Fu comic
Penelope and Circe from The Odyssey
Effie from “The Maltese Falcon”
Kinsey Milhone
Sand Saref and Silk Satin from “The Spirit”
Cordelia Gray from P.D. James’ novels “An Unsuitable Job for a Woman” and “The Skull Beneath the Skin”
Elizabeth Bennett from Jane Austin’s “Pride and Prejudice”
Two Doc Savage heroines: Hannah the Pirate “Mystery on Happy Bones” and Toni Lash from “The Devil Genghis”
Dr Julia Hoffman from Dark Shadows
Cirocco Jones from the Titan trilogy
And, Maggy, I gotta go with Meg Murry’s mom.