According to the Jewish sources we read, it is permissible to "skype into" a service to join in with a minyan to pray or say Kaddish along with them.
However, it is not permissible to actually form a minyan in cyberspace from different computers; rather, there has to be an actual physical minyan already praying in one place, and if there is, then you can join in with them on Skype (or Facetime, etc).
Why do you think Judaism places such an emphasis on praying together with a group?
One purpose of saying the Mourner's Kaddish aloud in a group is for a mourner to receive support from the community. Do you think it's possible to get comfort from other people if you're just skyping in, and you're not actually there in person with the other people in the minyan?