Can anyone suggest some good materials for learning more about the Linux filesystem and command line? I have found myself frequently confused as to what programs go where on the Linux filesystem. I would like to learn how the various directories (var, etc, usr ...) are used and how to use the commandline more effectively.

I come from the Windows development world (.NET developer) so I am very familiar with Windows system administration. However, when doing more and more work with PHP I found myself lost in the internals of Linux (specifically Ubuntu). For example I was having problems installing PEAR properly on my Ubuntu system and not understanding why it was installed where it was.

All of my interactions with Linux machines is done via SSH so I would like to focus on the command line and the filesystem. Thanks for any suggestions.