Basically you need three Linux partitions for this and you choose the last
option in the partitioning part of the installer, to do it manually. You install
Ubuntu to one partition with the mount point / for root. The second partition
will be a tiny swap partition that should equal but not exceed the amount of RAM
and it has its own format. The third will be for home and the mount point will
be /home. You can choose your file type for the format. Use ext3 or ext4 (for
Jaunty). I have found that you need more space for your home partition than in
the root partition. How you split it is up to you. Just leave room for growth.
You always need more than you think.

When you choose your user name it will create a user directory in /home. This
will be what you will use for whatever distro that you have installed. When you
want to re-install, you repeat the steps above, but do NOT format /home. You
choose the file system as ext3 or whatever, but make sure that the format box is
unchecked. When you get to user name, then you input the same thing as before.
This re-uses the user data and your desktop settings, bookmarks and email
accounts remain intact. It is a good idea to back up just in case, especially
the hidden files found in your use directory.

You can even save your package list and re-install the same packages so that
your new installation is identical to the old one. See:
http://ubuntuforums.org/showthread.php?t=1057608
http://ubuntuforums.org/showthread.php?t=479071