The home directory is the users home directory, as specified by the OS you are running. If you are using a *nix based system, the value of $HOME is used, such as /home/username. If you are on Windows, ususally C:\Documents and Settings\username\netbeans_user. Netbeans stores lots of info about the projects you are working on in this location under a sub directory, such as /home/username/.netbeans/5.5/.
If you want to change where netbeans stores all of it's info, pass the "--userdir path" option to the executable when starting. Note that the "path" you pass in will contain the files, Netbeans will not create a specific sub-directory in this location, so you will want to make a sub-directory just for Netbeans and pass in its path.