Emacs Directory Structure
The following is pretty basic information that shows how I setup Emacs.  This directory structure works very well for me when combined with my configuration file.  Therefore, if you are planning on quickly grabbing my .emacs configuration file, you will probably have to setup some if not all of the directories shown below.

Home directory
The only thing to note about a home directory is that under MS-Windows you have to set the home directory environment variable named "home" by hand.  This directory will contain files like .emacs, .netrc, or .Xdefaults.  Under NT you can goto the control panel's system option and select the environment tab.  From there, set the variable name and value.

Packages directory
I created a directory for packages at the same level as the site-lisp directory.  I then place the third party lisp files and lisp packages within this sub-directory.  I don't use the site-lisp directory because Emacs automatically adds all sub-directories within site-lisp to the load-path.  As I want to be able to add a new version of a package without disturbing the currently installed version, I need to be able to define the load-path with more precision.  This is where "config-site-lisp-path" variable should point to.

Backup directory
The backup directory is used as a central repository for backup files.   This avoids the hassle of cleaning up all of the files ending in ~ after weeks of development.  I place the backup directory within an emacs sub-directory below my home directory.  This is not fool proof, however.  As all of the backup files will be going to one directory, working on files with identical names will have identically named backup files and the backup result is unpredictable.  It is also worth noting that you will have to clean out this directory every once in a while.

Visual of the directory structure
The following should show an example of a possible directory structure that will work with my .emacs configuration file.

Hard Drive
Emacs Installation Directory
bin
etc
info
lisp
site-lisp
packages (Packages Directory)
dlgopen
Hard Drive
Emacs Installation Directory
bin
etc
info
lisp
site-lisp
packages (Packages Directory)
dlgopen
older.png" border="0" width="32" height="32" /> elib
jde-2.2.4
mmm-mode0.4.6
pcl-cvs-2.9.9
semantic-1.2.1
speedbar-0.12
site-lisp
packages (Packages Directory)
dlgopen
32" height="32" /> blinking-cursor.el
calculator.el
CUA-mode.el
extra-java-font-lock.el
gnuserv.el
site-lisp
packages (Packages Directory)
dlgopen
c="images/file.png" border="0" width="32" height="32" /> hl-line.el
hhm-config.el
html-helper-mode.el
CUA-mode.el
extra-java-font-lock.el
gnuserv.el
site-lisp
packages (Packages Directory)
dlgopen
htmlize.el
jsp-html-helper-mode.el
python-mode.el
recentf.el
strip-whitespace.el
site-lisp
packages (Packages Directory)
dlgopen
-serif" size="-1"> swbuff.el
tempo.el
ws-trim.el
tiedemma (Home Directory)
emacs
bak (Backup Directory)
.emacs
olspan="2"> site-lisp packages (Packages Directory) dlgopen ze="-1"> swbuff.el tempo.el ws-trim.el tiedemma (Home Directory) emacs bak (Backup Directory) .emacs olspan="2"> site-lisp packages (Packages Directory) dlgopen