If they were licensing why would they be in court with S3 and why would the judge rule infringement - http://www.bloomberg.com/news/2011-07-01/apple-gets-mixed-ru...

Is it possible that Apple's patent suit against HTC is a retaliation against S3's patent suit agents Apple? And if so, would it make it pretty silly to be freaking out about Apple trying to patent Android out of existence?

You will have to look at the dates - specifically date on which Apple filed lawsuit against HTC and also when S3 filed one against Apple - before or after they were bought by HTC.