Patents have a lot of "advantages" over normal publishing: investors like them, companies encourage them (as in, "if it's patented then it's a great thing for the company, if there are no patents it's not really "ours" so we're going to be more secretive about it, making it unusable in business situations where disclosure to other parties is unavoidable), you can publish something really obfuscated without really driving attention to the details or giving away much useful information, you want a larger portfolio to appear "dangerous enough" to a competitor who might otherwise want to sue you, etc. Combined with the fact that neither decision-makers nor patent examiners really understand patents, you get a lot of pressure to just go ahead and file patents and you are not unlikely to choose to do this as a part of advancing your ideas within the company.

One thing I recently encountered for the first time was the idea that a software-based product, when sold as an asset to another company, can only be treated as a capital gain if patent rights are being sold. Otherwise the sale is apparently taxed as ordinary income, for which a much higher rate applies.

I'm still not sure if my CPA was entirely correct when he told me about that, but if he is, it artificially inflates the importance of software patents in a big way.

Clear this up for me please. How does that help? Isn't that essentially the prior art thing that still has to get resolved in the courts?

Yes, but it changes the dynamics. If the defendant can point to solid prior art, the patent troll will likely beat a hasty retreat. The last thing they want is to have their weapon taken away from them by the adults in the room.

Thanks! Though that still seems more expensive than filing the patent.

Prior art is usually resolved by the patent office (or the patent trial and appeal board). It's only after they rule against you that you can take it to the federal circuit.