One of my favorites is the entire "His Dark Materials" series. tHe movie that came out a few years ago really trned people off from reading the whole trilogy, but they're very good. Also, try "The Night Circus" or "why We broke Up".....good stuff. :)
Umm... Miss Invisible was a favorite of mine. Honestly, I fell in love with Laura Jensen Walker as an author. She's fantastic for women in their older teens and twenties. :)
I am never certain how well known House of Leaves actually is. That's what comes from being so immersed in internet communities. If you haven't read it, the book is so strangely wonderful and uses a meta formula that jumps right off the pages and into your mind, destroying both.
After by Amy Efaw
Bunheads by Sophie Flack (not related to the new show)
Model by Cheryl Daimond
North of Beautiful by Justine Chen Headley
The Disreputable History of Frankie Landau-Banks by E. Lockhart
Handle With Care by Jodi Picoult
Peeps by Scott Westerfield
Sleeping Freshmen Never Lie by David Lubar
My Life as a Rhombus by Varian Johnson
I don't know how "undiscovered" any of these really are - I tend to like popular books and I know some of these are very well-known authors. Also, this list is a bit mixed. Some are books I read in middle school, others I'm reading in college. Some are sci-fi, others autobiographical, some are light reads while others really make you think.
Handle with Care is one of my favorites. Peeps is really good too, and everyone focuses on his "uglies' books so much! :)
A Need So Beautiful
Gone Gone Gone
Kiss the Morning Star
When the Sea is Rising Red
Masque of the Red Death (a novel, not the original by Poe)
who is ready for the new artemis fowl book TOMORROW?!?!?!?!? Nook FTW!
Sarah Diemer is brilliant in her portrayal of lesbian relationships. I am especially fond of The Dark Wife.
Some of my current favorites are Ella Minnow Pea, Sarah's Key, The Poisonwood Bible, Nailed, and Shattering Glass. I'm not sure how undiscovered the books are, but they're the ones that when I talk about them most people haven't heard of them.
His Dark Materials is a wonderful book series and I feel like it doesn't get enough love.
Paranoid Park is one, if you're into suspense and that sort of thing. As for high school romance, one of my favorites is this book I got cheap on my Kindle called "Cross My Heart."
This is quite possibly the best collection of "in your pants" titles ever. Linky-link