The /usr directory is the main application storage directory. All the binary files in this directory must not be required for the system startup or maintenance, since the /usr hierarchy is very often a separate filesystem. Given its often large size, /usr has its own hierarchy of subdirectories. We will mention just a few:
/usr/X11R6: the whole X Window System hierarchy. All the binaries required for the operation of X (including the X servers) and all the necessary libraries must be located here. The /usr/X11R6/lib/X11 directory contains all aspects of the configuration of X which do not vary from one machine to another. Specific configuration for each machine is in /etc/X11.
/usr/bin: this directory contains the large majority of the system's binary programs. Any binary program which is not necessary to the maintenance of the system and is not a system administration program must be located in this directory, apart from programs you install yourselves, which must be in /usr/local.
/usr/lib: this directory contains all the libraries necessary to run programs located in /usr/bin and /usr/sbin. There is also a symbolic link /usr/lib/X11 pointing to the directory which contains the X Window System libraries, /usr/X11R6/lib (if X Window System is installed, of course).
/usr/local: this is the directory where you should install your personal applications. The installation program will have created the necessary hierarchy: lib/, man/, etc.
/usr/share: this directory contains all the data required by the applications in /usr, and all the independent architecture data. Among other things, you will find zone and location information (zoneinfo and locale).
There are also /usr/share/doc and /usr/share/man directories, which respectively contain application documentation and the system manual pages.