I'm pretty happy with Windows 7 - there isn't a whole lot I'd change.
I'd like to see some improvements in Virtual PC - the ability to host 64-bit OSs and to use USB devices would be terrific.
I'd like them to put back a decent file associations tool, too. In XP you could create new context menu actions for file types but now you're limited to just adding programs to the "Open with..." list.
I'd also love to see a way to easily add customized start menus to the toolbar. Right new I have to do this with my own toolbars, and its a little hokey: