What do you want it to do?
In KDE, I have it configured so that the active window is the window that the mouse cursor is over. In addition, clicking on a window does not bring it to the front (you have to click on the titlebar to raise rather than just anywhere on the window). I can have a small window overlaying a bigger window and access the bigger window without having the small window disappear (such as if I have a web browser window on top of a word processing window for say, doing research).
I have never found a way to do this in Windows. The closest I found was a program called TXMouse but that doesn't work properly with Windows 7 (there are numerous unfixed bugs with the new taskbar involving parts of it that have incorrect window hints).