For Zoiper 3 you need to go to Settings -> Preferences -> Automation -> General -> "Catch the
'callto' protocol request from URL"
You can manage the protocol associations using the "Manage protocol associations" button below the checkbox.
Supported protocols are :
The best practice is to use zoiper: // telnumber since this way there is no interference with other application (Skype for example) for the callto entry.