At this point, you feel a little queasy, but probably not enough to quit your job... it probably doesn't seem like a big enough deal over which to quit. But, your boss is demonstrating that he does not feel queasy which means that if this trend continues, you may be doing something very unseemly for him before you know it. Ethics is a hard one because you need to work and minor offenses that your boss approves don't really reflect on you, right? You are doing what you are told and you even wrote something on Slashdot which should help clear you conscience.
That fact is that all companies do some unethical things (which is why companies should be highly regulated IMHO). We should consider what it really means though for you to follow orders in this case.
First, you are validating your bosses bad behavior and in effect telling him that he's doing a good job.
Second, you are encouraging other people to copy software.
Third, you are not taking a stand and demonstrating to others that your own ethics might be less-than-stellar.
Lastly, there is the legal issue. You might just go to jail.
Other than quitting, you can simply find out the costs, present them to your boss as a plan for upgrade, and give it to him every few weeks. That way, you are taking initiative, demonstrating that you care, and showing that most software doesn't really cost very much. Also, encouraging the company to use open source might just push him toward being more ethical and get you a promotion.