If you have an upgrade DVD and want to do a fresh installation-- you can, you'll just need to take a few extra steps to get the job done…

Start by booting the computer using the Vista upgrade DVD. Select the 'Install Now' option, but don't enter the Product Key (leave it blank) and deselect the option to automatically activate. Setup will ask you to confirm that you want to install without a product key entered; yes this is what you want to do. Now setup does not know what edition you are installing, so you'll need to tell it-- tell it the correct edition you have the upgrade (you will not be able to trick it, so choose the correct edition). Now, you'll get to choose the type of install and you actually want to choose 'Custom (Advanced)' install and not the 'Upgrade' install. At this point Vista will copy all the files and do some rebooting. When it is done, you will want to restart the installation process so you can apply your upgrade by rebooting the computer to the Vista upgrade DVD a second time. Click 'Install Now' and ensure the option to check for updates now is deselected. Now you can go ahead and enter your Vista product key (and again deselect the option to automatically activate). This time, choose the type of install you are performing correctly as 'Upgrade'-- now you are doing a proper upgrade. You may be asked to if you wish to boot from the DVD again, you can just wait a few seconds here and the setup process will continue on its own (no interaction should be required). When it is done, go ahead and activate your copy of Vista (you'll need to within 30 days unless you choose to extend the default 30 day period).