I know this list isn't complete, so if there's a book you know of that should be on it, mention it in the comments.
With one exception, the links go to the Indigo website, where you can learn more about the books.
I've put asterisks next to books I thought were especially good for one reason or another. And as usual with my reading lists, this is also a display at the World's Biggest Bookstore.
Swastika Night - Katharine Burdekin (writing as Murray Constantine)
Benefits - Zoe Fairbairns
The Carhullan Army - Sarah Hall
> Wither - Lauren DeStefano
> Birthmarked - Caragh O'Brien
> Anthem - Ayn Rand
> The Line - Teri Hall
> The Gate to Women's Country - Sheri Tepper
The Vaults - Toby Ball
The Fifth Sacred Thing - Starhawk
# Among The Hidden - Margaret Peterson Haddix
# The House of the Scorpion - Nancy Farmer
# Ender's Game - Orson Scott Card (I consider this more pure SF, but there is a birth cap and little adult presence among the chosen teens, so I can see how it made their list.)
# Partials - Dan Wells (I didn't add this to my list as I wasn't sure how much of a government presence exists, and it sounds more post-apocalyptic to me)
^ A Clockwork Orange - Anthony Burgess (I REALLY don't know how I missed this one)
^ A Scanner Darkly - Philip K. Dick
^ Akira - Katsuhiro Otomo
^ Ghost in the Shell - Shirow Masamune
^ Children of Men - P. D. James
^ Neuromancer - William Gibson
(books marked with > come from the fantastic Tor.com article Dystopian Birth Control by Caragh O'Brien and its comments. Which reminded me that Tor.com had a dystopia week, so I looked up some of those articles. John Joseph Adams, who edited the Brave New Worlds anthology, as a fantastic definition of dystopian fiction here. You can read some of the stories from the anthology on its website. Adams also hosted a round table talking about favourite examples of dystopian fiction, which lists several books I don't.
books marked with # are from this Flavorwire article.
and marked with ^ are from this article.)
Lee & Low Books has come up with a list where the protagonists/authors are from diverse backgrounds (people of colour, LGTB, etc.). You can see their list here.