I'm not sure when this happened exactly, but Amazon.com is now advertising boxed, retail copies of Windows Vista with Service Pack 1:
There are some interesting deals on various versions of Windows Vista here--Vista Home Premium Upgrade seems particularly cheap to me at $89.99, for example--but be sure to check out Amazon's hard-to-find Windows Anytime Upgrade page. This is the cheapest way to upgrade from one version of Vista to another, and now that Microsoft is no longer offering an electronic option (where you pay for the Anytime Upgrade online and receive a Product Key via email), a physical disk is the only way to get it.