Why is it all the advice is 'find a new job' or 'suck it up, and do what your told' and 'Your boss is the devil'.
When I started at my current situation, pirated software was rampant. It was really a situation that should not have happened but it was a person trying to save the company money. The cost to instantly convert the entire company over to licensed software would have severly cripled the company.
Together with the finance department we developed a strategy that allowed for licensed software for every new station and if new person started at a station we would buy a new license. On top of that we developed stategies to eliminate or reduce the software necessary, such as using a custom web application instead of an Access based system. IT department also stepped up the station turn over as alot of the existing stations were more than 2 years old.
In a short time we had removed the unlicensed software, and now have a better handle on who needs which software.
It is all about communication. Develop a strategy, and find ways for the company to remove the unlicensed software so neither you nor your company are in jeopardy of being in the unemployment line.