If this is limited to fictional geek girls, Kaylee. For real life geek girls, it would have to be Cat Schwartz.
Well, I was surprised to see Hoshi Sato on the list too, but I had to go w/ her in light of the massive crush I had on her when Enterprise first came out… That happened to coincide w/ my starting to study Japanese, and realizing, hey, there’re a whole lot of beautiful women over on the other side of the world… (and yes, I know Linda Park is actually Korean)
As for the alternatives mentioned, I would totally watch To Catch A Predator w/ Liz Lemon while scarfing down Sabor de Soledad… Even if she is quite a bit older than me…
Willow (Alyson Hannigan) was my fave from episode 1 of Buffy.
Then in the fourth season she decided she was gay and started dated Tara (Amber Benson)… I loved her even more. And Tara too!
Gotta’ be Temperance. I really don’t like Bones, but the analytic mind is hugely sexy. Hoshi is a close second, but the egregious omission of T’Pol is unacceptable.
ETA: So T’Pol was already mentioned. Doesn’t matter! Hot Vulcan chicks FTW!!!
I assume you mean . . .“to me” 
Cause I think she is and would totally do her.
Well you are certainly entitled to your opinion even if it is an opinion so shockingly wrong that it might indicate a dangerously disturbed individual.
Plus Liz Lemmon is one of the few characters who is legitimately “nerdy” (if you happen to like that thing) in the sense of dressing kind of frumpy and being socially awkward. The other TV geeks are extremely attractive women who are either on shows nerds like or play characters who are into things like engineering or forensic investigations.
Also, the OP did not include:
Gillian Anderson (X-Files) or
America Ferrera (Ugly Betty)
For the record, this is about “geek” girls - not “nerdy” girls - and there is a difference.
Also, I think Pauley Perrette (who I did vote for, Penelope Garcia notwithstanding) as Abby is hawt - but Pauley Perrette, MA in Criminology, as Abby is sooo much hawter.
After long and careful deliberation, Amy Acker.
Okay, who said that? WHO SAID THAT!?
I’ve never seen Chuck, so she didn’t occur to me. But to me, a geek girl is a female fictional character who has notable (and perhaps absurd) amounts of proficiency in a technological or scientific field; who is, while comely, either not conventionally so, lacks confidence or awareness of how good-looking she is, or feels herself over-shadowed by another character on the series; and who is either socially awkward or oblivious to the behavioral cues of others. Unrequited love also helps.
Willow is almost archetypical. For most of the series, she has no idea that she is incredibly hot, and I don’t think she ever believes it in her heart even after Oz, Xander, and Tara all validate it.
[joking] Daria [/joking]
Sara’s a spy - that’s about as far from geeky as you can get. I’m also having a hard time thinking of Kaylee as a “geek” too - she’s more “tomboy” to me, which is slightly different (but no less hot - in fact, probably more hot).
Had to go with Abby the lab geek. Although, speaking of lab geeks, what about all the ladyfolk on the various CSI shows? Some definite lookers there.
In the pilot episode of Firefly, Inara (Morena Baccarin) takes an onscreen sponge bath. Pretty hot.
Kaylee eats a strawberry. Infinitely hotter.
I’ll be in my bunk.
I must register a complaint, Jewel Staitye’s character is not a geek, not even close. She is a mechanic. Since when is being a mechanic the same as being a geek?
The hottest true geek on TV, even hotter than Kari Byron is Olivia Munn from G4’s Attack of the Show.
I completely forgot about Kari! Yowza! Pregnant women don’t do it for me, but I have to admit she still looks pretty good. I can still watch the older episodes, though. 
No one else has come forward, but with my vote I joined a small but growing contigent of Allison Mack fans (even though I haven’t been watching Smallville for the past couple of years).
Kristin Kreuk is so much more my usual type (dark and exotic), and she’s certainly hot, but there’s something about Chloe that always gets to me. I think it’s the smile and the eyes.
I just came in here to say this. I was thinking about it last night - there’s absolutely no way I can accept that Kaylee would be considered a geek. She’s mechanically inclined, not technologically inclined. Wash is a geek. Kaylee is a…gear head (I guess).
Geeks love her, but I have a strong suspicion she doesn’t love geeks.
Oh, come on. She’s hung up on Simon for the whole span of the series and movie, and - let’s face it, Simon’s a pretty big geek himself. 
Simon’s a doctor, not a geek. He’s certainly no Big Damned Hero, but he did also charge into a federal facility to rescue his sister - geeks stay in the ship and push buttons.
At first I was going to write-in Tina Fey (Lesbian Souryellowfruit on 30 Rock), if she counts as a geek. She’s age-appropriate too. But just before I submitted my vote I saw Jewel Staite on the list. She makes me quivery.
You’re just miffed cuz Kaylee’s kicking the butt of your choice! 