What you are asking is, for all practical purposes, to back up your entire installation to a thumbdrive. This article on the Linux directory structure might help make this clearer: http://www.tuxfiles.org/linuxhelp/linuxdir.html
If you place a new installation of something Linux on the hard drive after you format it, you are much better off installing your applications afresh, so that everything is consistent.
If a complete or almost complete backup is what you want and need prior to reformatting, you might want to look into cloning your system with Clonezilla
You are better off just backing up the configuration files for your applications. They are found in your /home/[username] folder in the hidden files and directories, that is, the files and directories whose names begin with a dot (period).
Before I reinstall, I back up the data (non-hidden files) in my /home directory, selected configuration files (that is, hidden files) from /home (that is, just the ones I've modified, such as my LibreOffice template, my Fluxbox configuration, and so on--not the ones still at default values), and any configuration files from /etc that I have modified (such as smb.conf and my rc.firewall script).
When you reinstall, you can restore the backed up configuration files and, when you start the applications, the previous configuration will be there waiting.
To be blunt, what you are asking to do is not an optimal strategy and very well might not be feasible.