I don't know of any applications, at least on the iOS App Store, that are able to even access the audio of a phone call.
From a quick search on the App Store, it seems the applications that do exist for iOS rely on workarounds where you either merge a call with their service or just dial out straight out using their application, neither of which would be working through the phone application itself. I would imagine it is a similar situation for most Android phones, as well.
I'm guessing these applications are allowed on the App Store since the liability would be on the side of the service provider, not with Apple.