Every once in a while I get a similar message from a new Mac OS X user: “Help, I've hidden a window from an application, how do I get it back?” Having freaked out the first time I accidentally hid a window, I know what that feeling is like.
The solution is easy (but not obvious)
Fortunately bringing back a hidden window is easy, if not obvious. Just go to the Dock, and click the application icon for the window you accidentally hid. For instance, let's say you accidentally hid a Safari window. Just go to the Dock, and click the Safari icon. Instantly your hidden window comes back into view.
Note that when you looked at the Safari icon in the Dock it had a black triangle beneath it. This indicates that the Safari application is currently running. (This is true in the "Tiger" release of Mac OS X, but this may change in the "Leopard" release.)
There are a couple of other approaches you can take to show your hidden windows, but this is my preferred method. My second most common approach is to use the [Command][Tab] key sequence to switch to a different application.