I needed to run multiple Skype instances on Mac OS X and here is the way to do it.
1. Create a new user from System Configuration > Users.
2. Login with this new user, might not be necessary, but I did it to see if everything is ok.
3. Go back to your normal user and open a Terminal.
4. Type su newuser. It will ask for the user’s password. Replace newuser with the user you created
5. Type /Applications/Skype.app/Contents/MacOS/Skype and the new Skype instance should appear in the dock
You have to leave the Terminal open, if you close the terminal the other Skype will close. Also note, that preferences and files are saved in the newuser‘s directory.
nohup /Applications/Skype.app/Contents/MacOS/Skype might also work to run Skype in the background so it’s not closed when the terminal is closed. Hope it saves you some time.