Here they are in order of publication:
1. The Maze of Bones
2. One False Note
3. The Sword Thief
4. The Cahills vs. Vespers
5. The Serpent's Shadow
6. The Black Circle
7. Beyond the Grave
8. The Dead of Night
9. The Emperor's Code
10. The Viper's Nest
There are also several spin-off series, which add additional books to the overall 39 Clues universe.