VLC and probably Banshee will have folders inside the .config file located in your home directory.
Nautilus will save certain settings (bookmarks and view options, etc.) in the .gnome2 folder, also located in your home directory.
I'm not sure what kind of "user data" you think is there for Synaptic, but you'll find that in a folder named .synaptic located in /root
I would be very, very careful about messing with anything in that folder; the potential is there to do great damage. Consider yourself warned.
AMD Phenom II X6 1045T 2.8GHz 8GB DDR3 RAM ATI Radeon HD6970