I've been thinking about this idea and by re-phrasing your question, "Why are certain people special?". I think you can make this a more general case than just one person working in a narrow field. But I'll confine my observations to the technology world and software world specifically.
So why are certain people special?
Maybe it has the same reason that in the past "what made them so un-popular".  The intellectual curiosity, ability to see change to "what is possible" instead of what is common practice. Seems harmless doesn't it? But a core mindset of questioning current practice and suggesting a new possibility instead of blind acceptance is threatening and outright dangerous talk to followers. I've observed that in certain types of decision making there are "leaders" and "followers". I'm pretty sure there is a good reason for it. From birth to the time you are old enough to go out into the world you generally accept what you are told is "the right way" to do things. This works for routine decisions like cleaning your teeth, twice every day to avoid decay. For a fair percentage of the population, doing what you are taught, told or pressured to do is pretty much the norm. Don't question why? Follow the standard procedures, get the job done. We need this type of thinking and obedience so we don't fall into chaos. Life is complicated enough without having to make hundreds of non-trivial decisions every week. What about other non-trivial decisions?
- Leaders, followers: Sometimes you have take lead in order to change. There are some that recognise you can improve a process by changing it. Then make those changes, Going against the norm, bucking the system. Continuing change in the face of criticism. You can see this clearly in Art. Whole art movements can be turned upside down by one group or individual artists exhibiting paintings. Science & technology is fundamentally driven by change and what is new. Old ideas are swept aside and new industries created when the fundamental understanding of a new idea is made public through experiments, papers and media. Usually by individuals, never whole teams.
- Communication: The ability to get an idea across is probably a good idea. So anyone who write, speak and argue rhetoric is a good bet. The Internet has really expanded this ability to communicate. Before the Internet, you had to read great ideas filtered through the whims of Journalists in your local newspapers. If you where lucky (or if the writer was lucky) you might read their ideas in Journals or trade magazines.
- Makers: Building your own tools is another. I don't what it is about having to make your own tools. Maybe it's the "dog-food" syndrome. Something inside makers that compels them to think up new ways to do things. Making you own stuff also keeps you humble. If you build your own things, you have a greater understanding of what you think and talk about. Less prone to the fancy talk of speculation. 
- Scepticism, cynicism: Take an idea, problem or situation, as is. Critical questioning the validity instead of trying to take the cheap route of downplaying a good ideas with cynicism. Instead propose a viable alternative. There is a fine line between scepticism and cynicism. The former if taken on the chin allows you to improve. The later as a means to destroy and denigrate.
- Generosity or meanness: When was the last time Bill Gates wrote about business, software or gave something away for free? I hear Steve Jobs hasn't got the time so he employs a "blog double" to write on his behalf.  In a gift culture, the generosity of the written word, software or ideas displays a "special quality". Show don't tell. Show through speech, the written word, software. These things are free but rich to consume.
- Smashing the 'status quo': In technology, there is more reward in making new things instead of re-hashing the old. New ideas and movements in technology are periodic. They come and go. So being able to not only question the "status quo" but smash it open is a bonus. This is the most dangerous quality. It's easy to follow. It's much harder to put you time, effort and reputation on the line.
Some people in the tech-world who have these "special qualities". To some degree or another I'd include Phil Greenspun, Joel Spolsky, Richard Stallman, Bruce Perens, Brewster Kahle. There are probably others that I don't know about. But these are the qualities I'd look for.
Of all the qualities I observe, I think smashing the "status-quo" is the most admirable. There is something "deliciously subversive" in not answering to a "boss". In not having to work at the yolk of another's Company. To work on your own ideas, in your time. Instead of someone else's half baked ones at times they set. Then try to profit from them. To question the very nature of what is considered "traditional work".
That idea alone makes Paul Graham special.
 Take for instance the amount of blogs on google appengine. Most are speculating and not talking about the problems building applications.