A daemon is a UNIX application that runs in the background as a process and once started, is always running even if the current user logs off. Daemons are most often started at boot time by the kernel according to its startup files. These daemons run as root, which makes them only able to be terminated by a user with super user capabilities. Examples of root daemons are the built-in web server, apache and the ftp server. Other root daemons can be added, such as a DNS server or Samba, a file server for windows clients.
Most applications operated by users are simple commands or small applications.
Every command typed in the CLI is a UNIX application. More UNIX commands can be added by compiling them or by downloading the binary and placing it in the application path. These applications must be compatible with both the system they are running on and the shell they are running within. By using UNIX scripting, a user can execute several commands with a single command. This is what happens, for example, when a user runs an install script.