If you've found this article, I don't have to give you a primer on Bilski. By the time the SCOTUS is through, we should have a much better idea of the metes and bounds of what kinds of intangible intellectual property is patentable.
Given the tart comments by the various justices at the hearing on the viability of busines method claims -- from Justice Scalia's speculation about the availability of "horse whisperer" patents in the 1840's to Justice Breyer's wishing he could get a patent on his technique of teaching antitrust law to sleepy law students -- it appears that there will be a drastic narrowing of the scope of allowable business method patents that do not involve computers.
Now, in the courts, you don't really see the kind of business method patents you see in Bilski -- hedging risk in commodities trading. So, if the Bilski ruling does nothing more than strike down those types of patents, it may have little effect on big time patent litigation.
However, if some, like Red Hat, have their way and software patents are substantially weakened -- or even eliminated -- this could have a huge effect on the damages a plaintiff might be able to get for infringement of a method claim. Especially if that method is normally performed by software. Especially if that method can be performed by open source software.
For the most part, damages are awarded in patent cases based on what the jury finds to be a "reasonable royalty." That royalty is determined by looking at how much the infringer would have paid to license the plaintiff's patent if the parties had met and negotiated when the infringer started using the plaintiff's technology.
The more valuable the patented technology was to the infringer, the more he would have paid for the right to use it -- and the higher the "reasonable royalty."
If, however, the infringer didn't really need the plaintiff's technology or it didn't give him much economic benefit, the infringer would not have paid very much to license the patent and the "reasonable royalty" would be quite low.
One big reason that the infringer might not have put much value on the patented technology, is if he could have acquired that same -- or similar -- technology (which did not infringe) from some other source for less, or even for free; thsi is known as a "non-infringing alternative." If -- as in the Red Bend v. Google case recently filed -- the defendant could convincingly argue that he could replace the patented techology with free open source software, the "reasonable royalty" may well be minimal -- or even zero.
Now what does this have to do with Bilski?
If the Supreme Court weakens or elminates software patent protection, this will dramatically increase the viability of free open source software, as companies like Red Hat will largely be able to operate without the constant danger of being sued by a software patent plaintiff. The open source industry will no doubt take full advantage to increase their "market share." Tux the Linux Penguin will have a party!
So what happens to your damages case if you own a patent and are suing on a non-software method claim that can be implemented in software? And what if a similar function is performed in a non-infringing way in some piece of open source software that came out of the post-Bilski flood of open source? And what if the infringer could just pop that open source module into its product and perform the same function as claimed in your patent without losing a sale?
As Tux would say -- You're fragged and you go home with nothing.
Think this can't happen? Watch the skies for the Bilski decision and wait.