Stephen King summed it up perfectly in a review of “Lawnmower Man”:
“In Hollywood movies, geeks aren’t ever really unsightly. They just have bad haircuts.”
Eww.
Eh, different strokes I guess.
Mr. Darcy from “Pride & Prejudice” - he’s arrogant and elitest, but his internal struggle and character growth make him…hot.
Jamie Frasier from the “Outlander” series… he’s a man’s man - he can hunt and fish and fight, but he’s also a Renaissance man - well educated and articulate. And he’s a tiger in bed. Mmmmm.
Stephanie Plum from the “One for the Money” series - she’s a dingbat, she sucks at her job, but she’s down to earth and hard as nails but mushy, too.
Oh, and while we’re on Buffy, allow me to nominate…Giles. 
I remember this hot French-maid sort of outfit she put on-oooh mama.
I recall a teen movie from the 80’s where there was a geek girl with gorgeous, straight, waist-length black hair. When they give her the inevitable makeover they hack off at least 2/3rds of it, style it into a 'do, ditch the glasses, and pronounce her “hot”. Guess I was the only one who preferred the “before” picture…
As long as we’re throwing around “Buffy” references, Jenny Kalendar (Robia LaMorte)…
I think a classic character that fits this bill is Melody from Josie and the Pussycats. Heck, many a gag was built around this fact!
(Although, to be fair, not only did she not know she was [considered] hot, but she didn’t know a heckuva lot more…)
Natalie Wood in “Gypsy” when she looks in the mirror and says “I’m a pretty girl, Mama.” Well…DUH. You’re Natalie Wood.
The example that I immediately thought of was Gadget from Chip 'n Dale Rescue Rangers - Chip and Dale were always fawning over her, but she was completely oblivious. She also often shunned attempts to appear even more attractive - and, as I once saw noted by one fan of the show, Chip and Dale collectively appeared in typically female attire more than she did.
As an aside, I always wanted to be Gadget when I was little - not because everyone had a crush on her, but because she could start off with any pile of junk and create amazing inventions in no time. Nerds rule 
I just finished watching the first season of **30 Rock ** on Netflix and I agree with you 100% She is so much sexier than Jenna.
Oh, she knows!
I believe that characters name was 6 of 9, seriously
Heh…would you believe she’s the character I was coming in here to suggest?
Merry Gentry of the Merry Gentry series tends to have trouble believing she’s good looking, due to constantly being told as a child and young woman that she wasn’t.
Honor Harrington of the Honor Harrington series considered herself unattractive for the first few books. Partly because she felt overshadowed as a girl in the beauty area by her very pretty mother; partly because 3rd generation prolong ( a life extension treatment ) has the unfortunate side effect of extending that awkward adolescent look for a decade or more, which shaped her self image; and partly due to several unpleasant early experiences with men.
Karrakaz of Tanith Lee’s The Birthgrave spends most of the book thinking she’s hideously ugly, when in fact she’s superhumanly beautiful. The few times someone sees her without a mask, she interprets their stunned reaction as horror. She’s also amnesiac and suffers from hallucinations and has supernatural powers which she doesn’t know the extent of and which have been hijacked by her subconscious traumas; sort of like Forbidden Planet’s Monster From The Id but more subtle ( and persecuting her as much as anyone else ). Which explains why she takes so long to figure out the truth.
I think Uma Thurman looks like a face painted on a duck egg.
In The Last Unicorn, the unicorn at one point is magically transformed into a beautiful woman – but she thinks she’s ugly, until Shmendrick and Molly Grue point out to her, “You could not be more beautiful than you are and still be human.”
Ouch, I’d forgotten that. Go to hell Shmendrick and Molly! Some of us like our women human!
(And what kind of name is Grue anyway?)
Let’s look at the evidence:
http://msunderestimated.com/GarofoloGrease.jpg
http://www.dosomething.org/files/Images/uma_lookingback.jpg
These were just the first two pictures I found. I am sure we could find even more evidence that Garofolo is a beast and Thurman is a goddess.
http://www.betterthanfudge.com/img/janeane.jpg
http://www.fortunecity.com/boozers/cheshire/60/jg39.gif
My rebuttal, sir.
A scene in The Breakfast Club had Molly Ringwald doing a similar thing to Ally Sheedy.