In Windows I can align Windows horizontally or vertically by right clicking the taskbar and choosing the menu option to do so. This is in Windows 7 and was probably in Windows since the taskbar came out in Windows 95. in Windows 3.1 there were buttons in the task manager to do this as well.
The thing is I have never figured out how to do this in Linux. I am really used to using that option when copy files files, I open an Explorer Window (or Nautilus window in the case of Linux) for a folder, then open another one and align them and drag files to move and copy files.
how the windows are arranged is governed by the so called "window manager".
There are several around. X window manager - Wikipedia, the free encyclopedia
So maybe you find one that better fits your taste.
As you mentioned Nautilus, your default WM is most probably Metacity.
If by any chance you use Compiz, there is an align plugin that does add this.
Or maybe you try this programm:
tile-windows - Project Hosting on Google Code