Comic Book shows = Wonder Woman, Isis, Sci/Fi = Deanna Troi and 7 of 9.
She’s the ONE
Novels: Ghani from Dune.
Movies: Winona Ryder in Alien Resurrection.
[first-love]The Angel pilots from Captain Scarlet[/first-love] Don’t make me pick one.
Slightly later in life: I’m with The God of Muesli Bars and the China Guy Molly (stepping razor) from Neuromancer.
Jeena Maslo, from the short lived AD Police OAV series. (Not the unspeakably awful recent remake) She took on boomers with a KNIFE, for God’s sake. After one tore her arm off, she kept it’s arm after it was taken out and had it attached in place of her old one. She could do the long-distance-pistol-shot-from-on-top-of-a-distant-building-taking-out-the-target-just-before-it-wastes-the-‘hero’ thing. She liked to cool down from combat-mode by having sex. Her ex got turned into a cyborg killing machine. What more could you possibly want?
Close seconds are ex-prostitute-turned-bodyguard/assassin (considerably less trashy than it sounds, really) Sarah, from Hardwired, and ex-fanatic-military-turned-drive-mechanic from Voice of the Whirlwind. Walter Jon Williams seems to have a thing for the tall, athletic, competent, tough-but-still-very-slightly-vulnerable types. But then, who doesn’t, really?
Hard to pick. Sarah has a cybersnake, but Reese at one point wears a nurse outfit. Sarah’d been pretty heavily biosculpted by the end of the book, though, while Reese didn’t even shave her armpits. Both had betrayal issues, in that they tended to betray people. Sarah got more screen time, but Reese got her own follow-up short story where she shoots herself in the kidney. (Deliberately) I’m going to go with Reese, just due to overall competence, but it’s a close call.
I’d back either over Molly, that’s for sure, even if she does have a thing for geeks. 
Sylia Stingray, from the original Bubble Gum Crisis, had a superhuman intellect, designed form-fitting power armor with high heels, fought killer cyborgs, ran a lingerie store, and drove a ’54 Mercedes. (the one with the doors that open up) AND she had blue hair. If THAT isn’t The Perfect Woman, I don’t know what is.
The bipolar (bi-everything, really) version from the 90’s upgrade never quite pulled it off, though.
I had a crush on Lady Jaye back when I was just a little maru, but I’ve learned the hard way that very little of what I watched or read at the time was as cool as I thought it was. Besides, I’m not sure GI Joe counts as science fiction.
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“From low tech to ‘Die Hard,’ eh? Such a busy woman. Wish I’d worn a bra.”
The president of the colonies from the new Battlestar Galactica. When Adama wants to attack the Cylons and continue the war she quietly and calmly tells him:
To paraphrase, “I don’t know why I have to keep explaining this, the war is over, we lost. To preserve our race we must run and hide and never come back.” Not the words a warrior wants to hear but absolutely correct.
I hope we see more of her.
Well, I mentioned her in the other sci-fi character thread, but I’ll mention her again. I find Jessica Alba’s Max, in Dark Angel, utterly stunning and she kicks total ass. A bit of a stretch, but if you consider spy-fi as sci-fi, Peta Wilson’s Nikita, and Jennifer Garner’s Sydney Bristow rock too. I guess I just have a thing for tough-as-nails, ass-kicking babes.
Halle Berry’s character, Storm, in X-Men is also ranks very highly on my list.