The organization of a Linux root filesystem in terms of directories is well-defined by the Filesystem Hierarchy Standard
http://www.linuxfoundation.org/collaborate/ workgroups/lsb/fhs
Most Linux systems conform to this specification
- Applications expect this organization
- It makes it easier for developers and users as the filesystem organization is similar in all systems
/bin Basic programs
/boot Kernel image (only when the kernel is loaded from a filesystem, not common on non-x86 architectures)
/dev Device files
/etc System-wide configuration
/home Directory for the users home directories
/lib Basic libraries
/media Mount points for removable media
/mnt Mount points for static media
/proc Mount point for the proc virtual filesystem
/root Home directory of the root user
/sbin Basic system programs
/sys Mount point of the sysfs virtual filesystem
/tmp Temporary files
/usr
/usr/bin Non-basic programs
/usr/lib Non-basic libraries
/usr/sbin Non-basic system programs
/var Variable data files. This includes spool directories and files, administrative and logging data, and transient and temporary files

Basic programs are installed in /bin and /sbin and basic libraries in /lib

All other programs are installed in /usr/bin and /usr/sbin and all other libraries in /usr/lib
In the past, on Unix systems, /usr was very often mounted over the network, through NFS
In order to allow the system to boot when the network was down, some binaries and libraries are stored in /bin, /sbin and /lib
/bin and /sbin contain programs like ls, ifconfig, cp, bash, etc.
/lib contains the C library and sometimes a few other basic libraries
All other programs and libraries are in /usr

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