More formal:
* Enigmas
* Puzzles
* Mysteries (this is a bit redundant but can be used for emphasis)
* Conundrums
* Riddle
* Cipher
* Arcane knowledge
* Hidden truths
* Unsolved cases
More informal:
* Secrets
* Hidden agendas
* Unsolved puzzles
* The unknown
* The truth (used in a mysterious way)
* The big question
The best word to use will depend on the context and the specific meaning you want to convey.