Copying an SD card (cloning) is easy enough to do. On Windows you can use Win32DiskImager. On Linux and OS X you can either use
dd from the command line:
$ dd if=/dev/sdb of=MySD.img bs=32k
$ dd id=MySD.img of=/dev/sdb bs=32k
For OS X the device names will be different, also in Linux you need to check which /dev/sd?? it is.
Also in Linux and OS X there are GUI applications that can do it for you - the Disk Manager in OS X, and "Gnome Disks" in Linux.
That is only good for the actual SD card contents though. If you need to clone the actual Yún itself then it becomes more tricky.
Fortunately there are tools available to help you.
Details on how to create and restore a backup of an OpenWRT system (which is what the Yún is) can be found on the OpenWRT Wiki: http://wiki.openwrt.org/doc/howto/generic.backup
Note that again it requires a Linux or OS X (preferably the former) system to do it since it relies on the standard Unix scripting tools and commands that are lacking on a Windows system.
You may be able to do all the above on a Windows system if you make it look like a Linux system by installing Cygwin.