Once you installed Ubuntu or what ever desktop flavor. You can install any type
of desktop flavor using Synaptic. Once you install the desktop flavor. At the
boot splash screen. You can select at type of desktop. This option is located on
the bottom of the splash screen.

Since Wubi is a Windows Directory, if I read it right, then I'd try a Puppy
Linux Live CD and Mount the Windows Directory. Then copy your personal files off
to USB or to another directory in Windows temporarily. Afterward, you can copy
them back, if you want using Puppy or Ubuntu's file manager. Remember to
un-mount in Puppy and Ubuntu, the latter may need the Password to proceed, just
like most things, like downloads and updates.

Yes, I've done that before. I'm talking about entirely different versions, not
DEs.

You said "if I partition and install one of these, my Wubi installed
/home and settings are going to be safe, right?"

I think I've mentioned this a time before, but if not, here it is
again: Backup important files in your Wubi /home first. They SHOULD
be safe after your partition and install, but there is always the
possibility that something can go wrong. If you have nothing there
you don't mind loosing, go ahead with the install. Otherwise back up
first. The process to mount and back up is the same from a live CD as
it will be from a new install. As Joan pointed out, if you Use Puppy
for the backup, you can burn the files to CD, or use a USB drive with
any live distro to copy over just the really important things. You
may have already been clear on all of that, but I just wanted to make
sure you were aware there is a risk (albeit likely a small one) if you
don't back up before you begin repartitioning the drive.

Not a bad idea to backup important stuff in Windows, also.

For what it is worth, I have repartitioned windows to install linux on
7 different computers (and more than one repartition for several of
them) and have never had any issue with windows afterwards, other than
having to fix my windows MBR for Windows XP. On the two windows seven
machines, there was no hitch at all that I can remember.

As far as how long the partition and install takes, I would give it
between 20-30 minutes once you have booted to a live CD. You can walk
away, and it will wait for you where user input is required, but I had
a system freeze once that way. So best idea is probably to stay
nearby. If the computer somehow gets shut down during the install
process, you will have to start over.

I think I'm going to try an SD card. It's what I've already got, and the CDs
aren't big enough. But even the SD card is only 16gb, and my home partition is
25gb. Will I be able to back them up individually? That way I can save the
important ones. Or is it saved in one block?

"Backup important files in your Wubi /home first. They SHOULD
be safe after your partition and install, but there is always the
possibility that something can go wrong. If you have nothing there
you don't mind loosing, go ahead with the install. Otherwise back up
first. The process to mount and back up is the same from a live CD as
it will be from a new install."

Once you've mounted the Wubi drive as a loopback like you described
earlier, you will be able to transfer individual files. You will be
able to browse the drive in Nautilus just like you can browse through
any folders in Ubuntu. Look for the mounted drive under "Places" if
it doesn't show up on your desktop after mounting. If you want, it
should be no problem to fill up the SD card, then finish off with a
thumbdrive or whatever else you prefer, if there is still more you
want to copy.

Then consider these all as backups. Once the fresh install completes,
remount the Wubi /home, and copy the whole thing over to your new
/home. Also, don't forget to reveal the hidden files (Control+H in
Ubuntu live CD, or click on the eyeball in puppy) to make sure you
have the things relevant to your various settings.

I did the SD card too. Depending out your system. It may run as slow as a live
CD.

Just to clarify,, I think you are talking about running Ubuntu from an
install on a SD card, whereas the OP was planning to backup his existing
install to the SD card, then do a dual boot on his main drive. Correct me
if I'm wrong, I just didn't want the OP thinking there was something wrong
with backing up on the SD.

Then again, I may not be clear on what timmytheimpaler is doing, either! :)

I was thinking some thing totally different and I am glad
you caught that. Boy is my face red. Just think if I was a leader of a country
and my pants where pulled down. That is why the leaders of this world where a
belt. Well off I go! To a store to hoard up some petrol before I can no longer
drive to work. That is different topic. Shhhhs. Do no tell the oil companies.

Are you going to set up your new /home on a separate partition? There are
good reasons for doing this other than creating more space.