Hotkeys involving the Windows logo key are reserved by the system. New ones are added over time. For example, Windows 98 added Win+D to show the desktop. Windows 2000 added Win+U to call up the Utility Manager. Windows XP added Win+B to move keyboard focus to the taskbar notification area. And a whole bunch of new hotkeys were added in Windows Vista, such as Ctrl+Win which is used by speech recognition. (It's also a bit of a pun: "Control Windows", get it?)
The fact that these hotkeys are reserved is hard to find. It's buried in a bullet point a third of the way down the Guidelines for Keyboard User Interface Design document. It's also highlighted in the WHQL keyboard requirements right in the section title: "Windows Logo Key Support (Reserved for Operating System Use)". But even if you didn't find the documentation (and I don't blame you), the history of Windows clearly indicates that new Windows logo hotkeys arrive on a pretty regular basis. If your program uses one of those hotkeys, there's a good chance it'll conflict with a future version of Windows.