The “stand-alone” application, where the chatbot runs on a single computer, integrates mostly some sort of system interface, allowing your chatbot to control certain aspects and functions of your computer, such as playing media files, or retrieving documents. It usually also has a graphical component built in, as well, in the form of an avatar (often female) that enhances interaction, thus improving user’s experience.
Messenger Bots are created using the new Messenger API that allows a bot to send and receive messages. The Messenger Bots are essentially chat bots that you can talk to from the Messenger app. The conversations will of course be different than those you have with your Facebook friends. These bots are meant to help you get information for example you can ask the CNN bot to tell you give you the current headline news and it will fetch them for you.