If you are newer to Ubuntu and Linux in general, I'd recommend you visit the Ubuntu Manual Project
. You can download the manual for free, or buy as a printed book. Just beneath the "Download Now" button is the "Alternative download options" link. Press that, and you can download the manual for 12.04, Second Edition.
Another good book is No Starch Press' Ubuntu Made Easy
. Not available for free, but No Starch Press publish a lot of books on Linux and open source and I find them usually a pleasure to read and work through.
If you want to get better understanding of the command line, I'd recommend the Introduction to the Command Line
book. You can read it online for free, download it for free, or buy
the printed book.
When looking for a better understanding of the technical bits, like the package management system and such, the The Debian Administrator's Handbook
would be my recommendation. (As Ubuntu is based on Debian, much in this book applies to Ubuntu as well but not everything.) Again, you can read it online for free, download it for free, or buy the printed book. This is more technical than the other books, but I found it highly approachable and fun to read.
It goes beyond saying, but Linux Format is an awesome magazine to get a broader understanding about Linux and each issue generally brings me something new to try or delve into