Move an off-screen window back on-screen on Mac OS X
This method seems to work: click on the Window menu, then click Zoom
Haven't read through the whole thread but the easiest way I found was to change the resolution of the screen:
Go to System preferences » Displays and then change the resolution.
This will force your computer to render the display again and reposition all open windows. Then just switch it back to your original resolution settings and everything should be back in place.
Three ideas:
CmdF1 (or CmdfnF1 if you've configured your MacBook's keyboard to use normal function keys) toggles your displays between mirror mode and extended desktop. A side effect is that windows get moved around somewhat unpredictably. This might move the missing window to somewhere visible. This likely requires the external monitor to be connected though.
Turn on Spaces, hit the hot key to displays the spaces overview and see if your missing window outline is visible there. If so, drag it to where you want it to be.
Quit the application and relaunch. Definitely a non-ideal solution and not practical if there's unsaved work.