TweakWindow is a handy window enhancement utility with a wealth of options. You can set your own transparency options, hide, minimize to tray, roll up, place window always on top of all others, and make it 'ghost'. All of this can be done via hotkeys, though window's system menu or by adding appropriate buttons to the window itself. In addition to standard features, TweakWidnow offers unique capabilities, like an option to change window icon or title so that no one can just come over and see what program you are running. One-click window minimization to the system tray is a great option for software that are automatically launched upon startup but aren't currently used.
Window ghosting is a feature that makes a window topmost and semi-transparent. All clicks will go through that window to the one located beneath, but the ghost window can still be closed, minimized, maximized, and resized. Version 1.5 adds new options and fixes some bugs.