/etc : System wide configuration
/usr : This should store programs and documentation
/var : Short for variable, its mainly used for storing log files, mailboxes, and sending data to printers, etc.
/home/$USER : This is where your files belong, its roughly equivalent to 'My Documents' in windows. (Note that $USER is a variable that is replaced with your username). You can also get at this directory using '~' at the start of a path, for example ~/my-file.xls
It is possible to store your data in the other directories, but it has the potential to conflict with other software and you would also have to become the 'root' user (a super user that has no restrictions and can do anything). You should avoid being 'root' as much as possible since 'root' ignores all security restrictions.
Theres more information on the purpose of the directories at:
The information is intended for software developers but it describes the standard use of the directories quite well.