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Actually, this Skype icon has been in use since mid 2004 and was the first time Skype changed the icon when it introduced it's, wait for it, "OS X" version. Up until the OS X version of Skype, the phone call icon was a green upside down phone.
The 2004 Skype icon looks identical to what apple ended up trademarking for the iPhone App icon, except apple made theirs square instead of round. So the Skype argument is actually very good, except their icon was within the Skype program to make a call and not the actual Application icon to open Skype, as the iPhones icon is intended to open the Phone Application.
Either way, the color Green has always been used on cell phone buttons with a phone icon for making a call and red buttons with a phone icon to hang up/end a call. So I can see why other companies would make their call button green, just as apple did.