I want to integrate Skype APIs in my native app. Is that possible? I have Googled around and couldn't find a way to start. I know there are APIs available for Mac OS X.
Can I make use of those APIs for my iPhone app? I know it is possible, as many apps like Nimbuzz have integrated Skype APIs in their iPhone apps.
Skype has a Public API which you can reference. This page has a wealth of information on how to use the API and the various commands. There is no public framework which abstracts it any further so you'll need to investigate how to make the actual commands by deconstructing the various wrappers.
I don't think Skype wants to particularly bring their API wrappers to the iPhone because you'd be competing directly with their own application. They do provide Cocoa wrappers but those are in the form of a framework and you can't have your own custom frameworks in an iPhone Application (only Apple approved ones). Also relevant: Skype bans Nimbuzz and fring while faking stats