In what Folder are Dock Applications are stored?
The "links" to the apps are stored in the file ~/Library/Preferences/com.apple.dock.plist in the key persistent-apps with ~ being the "shortcut" to /Users/yourusername:



In the example above I expanded the entries for App Store  and Launchpad.  The only exception is the Finder.app. Probably it's a fixed entry "injected" by Dock.app itself.

Normally, each user has its own com.apple.dock.plist file.