Personally, whenever I see one of these lists, I look for fiction books. This is obviously a personal bias, but I find it hard to relate to someone whose life hasn't been mostly changed by works of fiction. In my view, those works are usually far more powerful than non-fiction about the same topics.
For instance, you can write about the duality of the heart and the mind at length, without ever coming close to the powerful argument of Narziss & Goldmund. And you can write about the cyclical nature of life till you're blue in the face (in the fingers?), but will you ever convey the sense of emptiness that one gets at the end of Marques' One Hundred Years of Solitude?
Non-fiction is useful, no doubt, but imho the truly great writings are in the fiction form.
I get a sense of emptiness when I realize that what an author was trying to tell me in some dreadfully long, dreary and depressing book could have been summed up in a page or two, and been much clearer to boot. But that's just how my brain works. I'm still proud, though, of telling my high school literature teacher the same thing and getting a bad grade for it.
A great work of fiction is impossible to sum up in one page. You can recount the exact plot of Infinite Jest but it won't give you anywhere near the same experience.
I hate philosophical fiction qua philosophical fiction. Any idea can be made to work in fictional form; the interesting question is whether it works in real life, and fiction has a way of obscuring that extremely heavily.
The work that really solidified my opinion of this was "The World of Null-A". It is based around the "General Semantics" philosophy (which, if you've never heard of, the name doesn't really help you know what it is: http://en.wikipedia.org/wiki/General_Semantics ). I like to characterize such works as: "Masses don't do X, aww, sad, it fails. Hero does X. Wow! Masses try to hold the hero down, but the mighty power of X shall prevail! Wow, X is awesome!" In the context of a fictional world, this is an entirely specious argument.
It is somewhat ironic that my final rebellion against this form was in the context of a work on General Semantics. It could be argued that rebelling against being manipulatively fed the ideas of General Semantics is in fact General Semantic's moment of glory. In fact I think they are good ideas, I just didn't think the fictional treatment of them proved anything.
Consequently, I have no interest in something like Atlas Shrugged, and I have simply read directly about Objectivism, as a for instance. (I am making no claims about it either way here, just using it as an example; actually I'm not particularly taken with it specially vs. more generic libertarianism.)
I can still enjoy such works on their own (the first sentence of this post is carefully constructed, it does not mean I hate all fiction that contains philosophy); the Dune series would still be in my top ten very easily, and in fact I agree with many of the ideas in there, including the ones tbray mentioned in that piece. I just do not consider them very good arguments or demonstrations of that idea; instead I enjoy the works simply as coming from an author that is aware of the ideas, refreshing in much the same way it is refreshing to read a work where the author actually comprehends economics, or military strategy, or science in general. (Star Trek being my canonical example of something that stands in opposition to all of those...)
And yes, personal bias too. Not trying to claim everyone should feel this way, except that I will make a weaker claim that if your only exposure to an idea is a fictional work, you probably should examine it much more closely before adopting it.
Another vote for One Hundred Years of Solitude. It's a great book on an almost utopian society grounded in Columbian myth that is finally enveloped by modern society. It's the one book that everyone in my family read.
For instance, you can write about the duality of the heart and the mind at length, without ever coming close to the powerful argument of Narziss & Goldmund. And you can write about the cyclical nature of life till you're blue in the face (in the fingers?), but will you ever convey the sense of emptiness that one gets at the end of Marques' One Hundred Years of Solitude?
Non-fiction is useful, no doubt, but imho the truly great writings are in the fiction form.