This book does a good job of explaining the InnoDB internals. I have found particularly useful the section where it describe in detail all the server variables affecting InnoDB. Although these variables are also in the MySQL manual, some of them have never been explained to me as thoroughly as this book as done.
The title claims that it is a InnoDB reference. If is more than that, as the reference part id covered in three chapters. The rest of the book gives useful advice on maintenance, monitoring, and troubleshooting.