Yes. You can backup your home directory. There are at least three special precautions you must take.
1) Make sure you backup the hidden files/directories in your home directory. This is where your per-user configuration is held. In gnome you can right click in the directory and choose "Show Hidden Files". In the console you can do:
The files beginning with . (dot) are your configs.
2) Not everything is transferable. If your new environment has a different file structure, etc.. then some of your config files may have broken file references. So, don't just blindly copy your old home directory to your new one
3) System-wide configuration is held in /etc. You may want to backup this directory as well.