I have tried the following steps, and it works smoothly to open multiple instances of Skype in Windows, hope this little contribution can help every one. Following are the steps:
Step 1 : Download updated Skype executable file from http://www.skype.com/intl/en-us/get-skype/on-your-computer/windows/ and install.
Step 2 : Goto Skype root file and create Shortcut on desktop( if it is not there ) (ex: "C:\Program Files\Skype\Phone\Skype.exe")
Step 3 : Right click on Skype and open properties.
Step 3 : Right click on Skype and open properties.
Step 4 : At the end of the "target" field put "/secondary" (ex: ""C:\Program Files\Skype\Phone\Skype.exe" /secondary)

Step 5 : Click on Apply and Ok
Step 6 : Now Click on Skype shortcut on desktop, login and Minimize it.
Step 7 : Now once again click on Skype shortcut on desktop and it will open new instance of Skype and you can login with another userId.
Step 7 : Now once again click on Skype shortcut on desktop and it will open new instance of Skype and you can login with another userId.