In the case of A, I utilize the Facebook SDK which relies on the Third-Party Facebook cookie passed into my application when it is loaded in a Facebook.com iframe. Could I build my application a little different to not need this? Yes, but this way is a little more reliable and secure. B.) Google Analytics breaks for IE users when your application lives within any iframe. It relies on Third-Party cookies to correctly track the users actions, and browser information.
I am a big user advocate when it comes to protection of personal information, but I really believe that unless users stop using IE (which is not going to happen any time soon), or P3P is depreciated by Microsoft then for now it is a useful hack to get around yet another IE pitfall.