Patents give an exclusive right to an invention -- not the combination of things. Copyright and design patents are probably the better tools to cover such combinations.
Apple has surely patent exchange agreements with Microsoft and IBM. But even with those the iPhone will violate at least a dozen patents of third parties.
Assume that you own a company that has actual products and a patent violated by Apple. You will probably not risk to claim your rights with Apple, because your products will certainly violate some Apple patents. At least it will cost you millions to clarify the situation.
This leaves only two other types of companies: Companies with patents and no products and Companies with a product and no patents. The first type are nowadays called patent trolls. I'm not sure how we want to call the second type: patent losers maybe.
Free Software Developers will have to do without a patent if they are notified about it. A good example are specific bytecodes used for hinting of Truetype fonts, which is covered by Apple patents. Look here:
Interestingly Freetype helped Apple to find new licensees for their Patents from embedded vendors. Meanwhile on distributions that care about patents your desktop experience will be hampered, because they use autohinting instead of the carefully designed bytecode.