I recall Steve at MWSF07 saying "..and Boy,have we patented that" or something similar, and I'm pretty sure he wasn't referring to the iPhone itself, it's not like they don't do the same for iPods. I think it's the way multi-touch has been implemented in the UI and such.
I think they have an application for the implementation, but it's for a specific algorithm. Like most such patents, it's easy to get around by doing something slightly differently. So when he said "boy have we patented it", that was mostly fodder for his fans. He is a very good salesman.
Here's a list of all granted Apple touch patents.
They also have a bunch of design patents... which protect the look of the cases, etc.