How do I manually uninstall Wubi?
Remove C:\ubuntu and C:\wubildr*
In Windows XP you need to edit C:\boot.ini and delete the Ubuntu/Wubi line. For Vista, you can use EasyBCD to edit the boot menu. Alternatively you can modify the boot menu via Control Panel > System > Advanced > Startup and Recovery and pressing "Edit". For Windows 98 you have to edit C:\config.sys and remove the Wubi block.
To remove Wubi from the add/remove list, delete the registry key: HKLM\Software\Microsoft\Windows\CurrentVersion
An easy method of removing this registry key is to paste the following text into a plain editor such as Notepad, close and save the file as something like removeWubiKey.reg (you may wish to go to Folder Options > View and disable the "Hide file extensions for known file types" option to check that the .reg extension has been applied correctly). Then you can perform the rest automatically by opening the file in the normal Windows manner, or choosing the "Merge" option from the right click context menu. Note: The formatting is rather strict, so copy the text exactly for best results. You may need to be logged in as the administrator to delete the key, depending on the version of Windows you are using. User Account Control in Vista may also ask for permission, in the typical fashion.
After deleting the registry key, Ubuntu may still appear in the program list. If this is the case, you may be asked if you would like to remove the item from the list.
How do I reinstall Wubi?
Run Wubi.exe again. Wubi will detect that there is an existing installation and you will be offered an option to uninstall. You may want to backup the installation files (the ISO) in order to avoid having to download them again. Note that when you reinstall, the system virtual drive (root.disk) is reset.
How can I make a backup of my Wubi install?
The easiest method is to to simply copy the root.disk to an external medium. In the event that something goes wrong, copy the root.disk back to the Ubuntu folder on the Windows drive. Note that this is not the most efficient method (since it copies the whole root.disk rather than specific data/settings) but it is effective.