Learning the basics of Linux/Unix

You might like the online guide - Introduction to Linux - A Hands on Guide - as a good starting point. Importantly, it is a well-structured guide. If this is not for you, have a look at Linux in a Nutshell and How Linux Works

A working linux system is typically an installation of a linux distro (distribution). At some point you're going to have to learn processes and commands that are specific to your distribution. You might as well choose a book or guide that bases its explanations and examples on the distro you're using or likely to use.

If you have the time and the inclination, you cannot go wrong with this comprehensive guide: LINUX: Rute User's Tutorial and Exposition. This guide is a blessing for someone who wants to understand linux, not someone starting out on desktop linux.

Here are some links to Linux tutorial sites. To learn more you of will need tutorials on the type of Linux you want to use. This might or might not be what you want:

http://www.linux-tutorial.info/

http://lowfatlinux.com/

http://www.howtoforge.com/

Tutorials on Ubuntu:

http://www.simplehelp.net/2007/08/13/linux-for-parents-a-beginners-guide-to-ubuntu/

http://www.unix-tutorials.com/tutorials.php?os=Ubuntu

http://ubuntulinuxhowto.blogspot.com/

http://www.ubuntugeek.com/

Please tell me if you would like links to other types of Linux tutorials.

This isn't quite what you're looking for, but I found the Gentoo Installation Handbook to be rather informative. It taught me a lot about how a Linux system is put together from a software perspective.

Reading on the net and following tutorials is fine, but I found over the years that user groups can also sometime be very useful. Exchange of information, and working with peers is sometime the best way to get your hands dirty about Linux.

And I also think that the best way to learn Linux is to actually start using it. With today's virtual machines, it is easy to get Linux installed in a way that will not cause troubles to your existing installation. Same for the live versions, such as Ubuntu. You can start everything from the CD, and even install it on a USB memory stick, so you can start from it, have your own setup and config, then with a single reboot get back to your existing comfort zone, in the the OS you use to do your work. Once you're comfortable enough with Linux, you can then make the jump and get it installed on your own hard disk. But by then, you will have gained experience.