Ctrl+Z is the Emacs command to minimize a window (Emacs calls windows “frames”). It is technically unrelated to the use of Ctrl+Z to suspend a command in a terminal window (but the shortcut was chosen by the Emacs designers because they are somewhat similar actions).
Normally, window managers display a list of minimized windows somewhere. Originally, “somewhere” was meant to be an icon on the desktop, which is why minimization is also called iconification. Many window manager provide some other way to unminimize a minimized window, for example by selecting from a list.
If your window manager doesn't provide this feature, you can do it from the command line. Very recent versions of wmctrl can do it with wmctrl -x -Y Emacs. Recent versions of xdotool can do it with xdotool search --classname Emacs windowmap.
If you started an Emacs server, you can restore the Emacs window with emacsclient -c '(make-frame-visible)'.
To avoid future mishaps, you can add the following lines to your ~/.emacs to get a confirmation prompt before minimizing:
(defadvice iconify-frame (around iconify-frame-confirm)
(if (y-or-n-p "Really iconify this frame?")
ad-do-it))
I don't override the C-z binding because it is useful in terminals. You may want to replace iconification with something else that's useful with Ratpoison. Also be sure to start an Emacs server so that you can issue commands with emacsclient: put (server-start) in your .emacs.