"In re Biliski" does not require something to be "a product" to patent it. There is no commercial success or commercialization requirement to get a patent. What Biliski requires is that the actual claim language for a process claim (1) is tied to a particular machine or apparatus, or (2) it transforms a particular article into a different state or thing.

technically ... sue them and either get a "reasonable royalty" or "lost profits." Lost profits being the profits that the plaintiff lost due to the infringement. Thus, IPAT will likely want a "reasonable royalty." See 35 USC 284. Damages only go back six years from the date the complaint is filed. See 35 USC 286. Thus, only damages for infringement going back to Dec 30, 2002 can be recovered if IPAT prevails.

There are also equitable defenses of laches and estoppel etc but usually there has to be unreasonable delay and reliance on the delay.

I have not researched this case in particular but it could be that the infringement recently started to occur, or started a handful of years ago and IPAT had tried to do this "nicely" but did not have luck. Maybe IPAT is in the wrong.

In any case, hopefully whoever is in the right will come out on top here.

People who are good at business get paid.
People who are good at programming get screwed?

My time, knowledge, and skill are not worthless and I would want to be paid. The GPL is great but FOSS programmers could exclude companies that use their software from the license and require an that those companies take an additional license so the programmer can get paid.

Also ... a software patent would be useful here ... and potentially beyond :)