Apple - How do I move a window whose title bar is off-screen?

Hold on option (or alt) while clicking the Window menu. This should change Bring All to Front into Arrange in Front, which did the trick for me.

This worked for me on OSX 10.9.1

Windows that support resizing from all edges can also be moved by for example dragging them horizontally from the bottom edge.

You could also try running something like this in AppleScript Editor:

tell application "System Events" to tell process "FileZilla"
    set position of windows to {100, 100}
end

In the case of Filezilla (for example) there is no window menu. You can however hold option while dragging the lower left or right corner of the window and it will proportionally scale the window (down in this case) and reveal the titlebar.