Waiting For The Barbarians JM Coetzee (I think that's spelt right) is my recommend of the moment, its fast become my favourite book of all time, I would also recommend some of Orwell's diaries and political writing, like The Road To Wigan Pier, its really interesting to read the reflections and internal conflicts which drove Orwell and his writing is very human and honest.
I've always liked the first of the Bourne books, the Bourne Identity, too and think its worth reading, I'm rereading it at the moment.
Fevre Dream by RR Martin (the same guy as wrote game of thrones) is an excellent book, very good alternative, almost sci fi take on vampire genre but deals with big topics, dreams and disillusionment, unlikely friendship.
Bring The Jubilee by Ward Moore, a different sort of time travel book, I liked it for the reason I like Waiting For The Barbarians and Orwell, its a sort of first person narrative and insightful and honest. It contains a big twist in the final couple of pages, steampunk before there was such a thing, in a world in which the US confederates won the US civil war.
The Cosmic Puppet's Philip K. Dick, a good book on a secret struggle between two cosmic demigods, could be fantasy, could be sci fi, just a great book about wandering into a real life adventure and having a string of WTF experiences. If you like this I'd check out Our Friends on Frolix 8 and Time Out of Joint, also good PKD books but not as well known as some of his books, deal with similar nothing is what it seems or "inner space" sci fi.
News From Nowhere William Morris, a pastoral paradise, the socialism which Morris aspired to was the total opposite of that espoused by others like Edward Bellamy, in fact News was written as a response and alternative to Bellamy's Looking Backward (most of which has come to pass). In Morris' alternative you could swim in the most polluted rivers because they're now clearer and cleaner than bottled spring water, people do construction work as a form of physical work out and the entire thing is based upon a collective desire for rest over riding all other priorities. The only downsides come in the shape of the decline of printing and publishing or culture, since people are enjoying free time in each others company and the sunshine so much more instead.