I'd have to say Aquaria.
It manages to combine most of my favorite things about games:
1. A charming world with tons of fun little side-activities/discoveries
2. A sense of grandeur and mystery about the world, and a feeling of adventure and exploration
3. Moments of pure horror
4. Actual challenge, without being just frustrating
The story is moderately interesting, but probably the weakest part of the game. The music and artsyle are gorgeous, the gameplay is fun and interesting (especially the singing mechanic), and the world is just amazing. And the fact that this entire 40-something hour game was made almost entirely by just two people is even more impressive.
People I know who played it really liked it, but most people I know never played it. Maybe they think it's some kind of casual girly thing, but it really isn't.