Can we make Web Apps in WordPress with specific (custom) scope, something like a mini-Facebook, a mini-Twitter, a stackoverflow, etc. What I really want to know is that how much am I free handed to build whatever Web App I want in WP? and more importantly how to?
Yes, of course you can make any type of web app.
Use Page Templates for different pages, Custom Post Types for different data handlers, Taxonomies for categorizing those data, and Plugins for advanced functionality.
WP Codex is best way to dive into WordPress.