Windows only: Freeware program HideWin lets you define a list of windows you want to be able to hide fast and completely from your desktop in the event that,
To use HideWin, you'll want to select the List Visible Windows options and find the class, title, or both of the windows you'd like to hide (the rule from the screenshot, for example, will hide Fleshbot). This may not sound impressive, since it may seem like little more than a Windows+D/M shortcut or a minimize, but in fact HideWin actually hides the windows from the taskbar, so they're not just minimized - they actually disappear.
The real bummer of HideWin, though, is that there's no keyboard shortcut available to automatically hide/show your defined programs, so it's more of a two-click affair. — Adam Pash