I've read tutorials where it says that it's better to have /usr and /home on separate partitions so if you reinstall, all your programs and settings will be intact.

So if I install programs in /usr and reinstall Linux....don't the programs store some kind of settings or files in other partitions/directories which may have changed after installing the OS...thus the program won't work? In windows, programs store registry settings and DLL libraries in System32 and other directories. So if you reinstall, you have to reinstall all your programs too.

Also for the settings, if I install gnome-panel...doesn't it replace the .panel files I have in the home directory?