All other things being equal--i.e. stable wifi connection--supposedly Apple's FaceTime technology is supposed to produce slightly better results than Skype's. The reason is that FaceTime is exclusively an Apple technology, so ALL devices involved in the conversation are running Mac OS or iOS. By contrast, Skype is a broader platform (though still proprietary) and so there could be much clunkier devices connected.

I like the elegance and simplicity of Apple's FaceTime--all I do is select a contact from my list who is eligible for FaceTime calls. There is no need to open up the Skype app, log in, check the connection quality, etc.

Just my $0.02.