I agree with the points that oderaro raised. One big difference though is the type of software package management software in use. If you are looking at RedHat certification then you need to know rpm, if you are looking at Debian/Ubuntu you need to know dpkg and if you are looking at a generic certification you need to know both.
The difficult thing is that there are so many books to choose from.
For my revision (for LPI) I've been using the Debian Bible published by Wiley, which I find is really useful if you using a Debian based distro (including Ubuntu), but it doesn't cover the RPM things. It is focused around command line commands, rather than the GUI.
On the other hand the RedHat Fedora Bible (sister publication) is much more GUI / Workstation based rather than server / command line. It is rpm based.
I've written reviews of those two books at:
http://www.penguintutor.com/reviews/, but I haven't got many other books to draw a comparison with. Unless you are specifically wanting a certain distribution you may want to look at a generic Linux book, but I don't have any (recent copies) to give a personal recommendation.
Personally I like a printed book as it's easier to read when convenient, but there are also lots of free online materials. I have started creating
Linux Tutorials (see the Shell / Basic Commands section), and there are some useful guides on
The Linux Documentation project such as the
Bash Beginners Guide
If you are a Linux beginner then I found it better to start with a GUI based setup, but then try and learn some of the alternative ways of configuring the machine using the command line.