But it still really bugs me that he calls himself a PhD, and asks for the title "Dr." (And yes, I have a PhD, on which I worked for 11 years, at great cost to myself and my family. So feel free to take my comments with a grain of salt.)
A PhD doesn't mean that you're a very accomplished person. Or a smart person. Or an influential person. It demonstrates that you know how to create, execute, analyze, document, and defend a specific research project, using the tools and vocabulary of a discipline.
If a university wants to retroactively award Stallman a PhD for his research, then they should do so. I know that this has been done in the past, because a professor in my graduate program got his PhD in precisely this way -- he did amazing work, and someone said, "You know, this is worthy of a PhD." He wrote it up, and got it. It's quite possible that one or more universities would be willing to do this for Stallman.
But until they do, his honorary PhD is a way of indicating their gratitude and respect for his many contributions to the world of free software. Which is great, but it's not the same as a real PhD.
By the way, MIT (where I got my undergrad degree) doesn't give honorary degrees: http://news.mit.edu/2001/commdegrees I'm rather proud of this, as well as the fact that when you graduate, you don't do so "with honors" and such. Either you finished, or you didn't.