Graphical interfaces have to provide usability to users. Many of us have dealt with GUIs that were not well designed; the issue is with either presenting the information in a non-intuitive manner or not providing the tools we need to accomplish a task. Sometimes, the designer of a program never actually uses the program. Often, what makes sense on paper doesn't actually carry over to the final user's interaction.
Some organizations have guidelines for GUI best practices, such as Apple's Human Interface Guidelines (https://developer.apple.com/design/human-interface-guidelines/macos/overview/themes/). In Apple's case, they provide directions for designing software for macOS, iOS, the Apple watchOS, and even Apple's tvOS.
Another example is the GNOME desktop environment (https://developer.gnome.org/hig/stable/). Other organizations or products have their own recommendations; Wikipedia provides a list of various guidelines on its Human Interface Guidelines page for different environments, as different vendors, operating systems, and software recommend, or require, particular interface configurations.
The purpose of these guidelines is to encourage the developers to use intuitive and consistent interfaces, particularly when designing a particular desktop or device environment. Thus, users can expect to find the same functionality in the same locations across applications.
One thing to recognize is that a GUI is normally a graphical wrapper around text-based commands. Every text command that a user can perform on a command line could also be handled by a GUI. Sometimes, however, it can take multiple user actions, such as mouse clicks, to perform the same thing through a single or a combined line command. Since people are visually oriented, more information can be conveyed via a graphical interface than a person could understand through text.
Most GUI environments use the Windows, Icons, Menus, Pointer (WIMP) paradigm; this is especially common in traditional desktop/laptop applications, as well as websites. Other GUIs can use different paradigms, such as heads-up displays in video games, or icon-based menus in mobile phones that don't have windows.