Examples I can think of:

Little Children (apparently)
That film when the really hot girl pretends to be a guy to get on some college soccer team
"She's All That" - any film that has as its central premise the fact that Rachel Leigh Cook's character is an ugly geek has got a problem right off the bat really (http://www.celebrity-bookmark.com/previ ... _28021.jpg - ermmmm.....)
British TV soap Hollyoaks - it's about a town somewhere in the midlands - I've never really watched it but it's basically lots of really hot looking young people (think the OC but less glamourous and set in a shitty english town), whenever they have a geeky character it's invariably some delicious brunette who they make wear her hair up and have glasses.
I did some wikipedia-ing into ugly betty and even the actress in that isn't too bad... http://eur.i1.yimg.com/eur.yimg.com/xp/ ... 388479.jpg
Velma in the scooby doo film (pretty much the most famous ugly, geeky chick in fictional history) was played by the extreeeemely foxy Linda Cardellini (http://images.askmen.com/galleries/actr ... ture-1.jpg)

I'm not sure what the conclusion to this highly scientific study is. I'm going to go with "fucking hell Rachel Leigh Cook is HOT". Something like that.

Oh, the soccer film was She's The Man apparently, where this girl (http://us.movies1.yimg.com/movies.yahoo ... anpre6.jpg) pretends to be a guy. Hmmmm....