An application can have a multiple web.config file,but in root folder must have a one web.config file i.e default web.config file & other each sub folder contains a single web.config file.So maximum web.config files must not exceed  numbers of subfolder + 1(i.e root folder)

Web.config file is configuration file for a Web application and stores various settings for an application. An application can have a single Web.config file only.

App.config file a configuration file for a Windows application and purpose is same as Web.config has for a Web application.

Machine.config file has settings that applies to the entire machine (means all applications running on a machine).