The most common way to type in command lines is via the terminal. On the terminal, one can enter any number of terminal commands to manually control the computer, from editing driver information to installing programs. Oftentimes, however, the intricacy of the commands are so technically demanding that many users become discouraged.
As such, there are also many programs that run within the terminal, from internet browsers to programs to configure the wireless. A shell within a shell, one might say. These are even easier interfaces for users to manipulate their system.
Of course, there are then programs that run yet one layer more indirectly—think of your internet connection software, or even up to such high level, front-end programs as Mozilla Firefox. All of these are, technically, shells—it just depends on how direct or indirect they are to interacting with the original kernel and the computer system as a whole.