Three at Once: titles like Tale of Desperaux, City of Ember, and The Series of Unfortunate Events.
If you are looking for a book like The Tale of Despereaux, you may like
Redwall by Brian Jacques.
The peaceful life of ancient Redwall Abbey is shattered by the arrival of an evil rat and his villainous hordes. Matthias, a young mouse, seeks the legendary sword of Martin the Warrior which he thinks will help Redwall's inhabitants destroy the enemy. This is the first of many books in the Redwall series.
Here is a possible match for City of Ember:
Gregor the Overlander by Suzanne Collins.
Eleven-year-old Gregor and his two-year-old sister are pulled into a strange underground world while on a quest foretold by ancient prophecy. They trigger an epic battle involving men, bats, rats, cockroaches, and spiders. This is the first book of a series.
Last but not least, if you liked Lemony Snicket's “Series of Unfortunate Events”, you may also enjoy:
Matilda by Roald Dahl.
Matilda applies her untapped mental powers to rid her school of the evil, child-hating headmistress and restore her nice teacher to financial security.