I had just read an article over on Slashdot about Microsoft settling a patent infringement lawsuit. What struck me about the article is that Microsoft's settlement involved paying the patent holder, Timeline, about $5 million dollars in exchange for licenses to the patents in question. This actually pours cold water over Steve Ballmer's claim that open source is not a respecter of "intellectual property", because the settlement shows that his company is just as guilty. In fact, on doing a cursory search, I discovered that Microsoft has been found to have infringed patents since 1988. And Steve Jobs' company is no saint either. Sorry guys, you talk a good game but the facts put the lie to your words.
So what can we do against patents? Under the current regime, not much. If you can't find prior art or demonstrate obviousness, you're at the mercy of the patent holder. In fact the patent system has spawned a new class of companies whose sole business model is acquiring patents, licensing them and/or suing other companies over them. These companies, known commonly as "patent trolls", are software companies' worst nightmare. They cannot be countersued, and they can even sue companies who have previously owned the patents given to them(aka backstabbing).
The only way to really get rid of the patent problem is to literally get rid of software patents. Think about it. Europe has done precisely that, recognizing that copyright, trade secrets and trademarks can protect software more than adequately and that software patents actually stifle innovation. There are no patent silos held by major corporations to clobber competitors with, and no patent trolls to worry about. Ideas would flow more freely and spur on innovation(which ironically is the reasoning behind patents in general).
So in the end, despite Steve Ballmer's patently ridiculous blustering, Microsoft may wind up standing with open source to oppose patents because it actually does make good business sense. Watch for the attitude change when Bill Gates formally retires next year.