While most people believe that patent trolls hold all the power in the current legal system with their ability to sue companies en masse without repercussion, it appears that that’s not entirely true.

There’s at least one troll that could be in for some serious pain in the coming months in Lodsys, everyone’s favorite troll to hate.

Last year in July, Apple filed a motion in the Eastern District of Texas, asking the court permission to intervene in lawsuits filed by Lodsys against iOS developers. Earlier this week, the court granted Apple’s request, meaning that the Lodsys legal team will no longer be paying an underfunded independent developer’s legal team, and will instead be going up against one of the most formidable patent-focused legal teams in the world.

This is not only good for the developers that are currently fighting Lodsys, but could benefit the entire ecosystem. With patent trolls like Lodsys and Intellectual Ventures and other non-practicing entities always on the lookout for good targets, the strategy is to normally go for firms that either have incredibly deep wallets, and force a license, or to go after indie firms and ask for a small percentage based license.

With Apple now defending its application developers, iOS developers will not be the handsome targets they were last year. Now, firms like IV and Lodsys will likely begin to look to competing platforms like Android and Windows Phone for attacking the developers. While the claims against each of these platforms may be as dubious as the current ones against iOS developers, what really matters here is perception.

Combine this with the fact that when developers create applications for Windows Phone and Android, they are actually creating applications for individual manufacturers, each of which have different licensing agreements with different patent portfolios. This raises the question of whether or not developers will release applications for some manufacturers, but not others, in an effort to protect themselves from legal troubles.

The perception could change from seeing Android as a quick-and-easy “open” platform, to one that allows patent trolls to sue developers left and right. For Windows Phone, it wouldn’t be surprising to see Microsoft go to bat for developers facing legal threats, but there’s also been no public sign that this would happen either.

That is why this decision by Judge Rodney Gilstrap could have repercussions across the industry. Consider developers that are deciding whether or not they want to release an application for iOS, Android, or Windows Phone. If you were developing an application, would you go with the platform that secures you from legal threats, or go to the one that is the Wild West, as far as patent law is concerned. Ignoring technical factors, that alone would make the case for developing for iOS.

Of course, this is a scenario that won’t play out until at least the end of the year, and likely not until the beginning of next year. Large shifts in perception take time, but if Lodsys and IV aim their sites on competing platforms like Android, you can be sure that how developers view potential platforms will change dramatically.

And all this being said, the party that is in for the most pain is Lodsys and other non-practicing entities. Fighting Apple’s legal team is going to be a pain, and with the eventual possibility of sanctions for trolling (not common, but not unheard of), this may end up hurting Lodsys quite a bit. As for Apple, what the company is doing is absolutely correct not just for the developers, but also from a PR standpoint. Microsoft and Google would do well to do the same thing, if they want to keep developers around.