One top contender from her list of SF that's really fantasy:
Anathem, by Neal StephensonRead about the other entries on the list.
It may be set on another planet and involve some of the most outrageously awesome depictions in literature of the scientific process - as well as hyper-realistic space travel - but Anathem's central premise is metaphysical rather than scientific. The "aliens" in the novel are not from another part of the universe, but instead from a dimension which is "less perfect" than those of the main characters. Stephenson tips his hat to many Western metaphysical theories in explaining this conundrum, which is a big hint to the reader that lurking beneath the hard science fictional armor of this plot is a story of cultural progress that relies more on philosophical principles than scientific ones.
Neal Stephenson made Charlie Jane Anders's list of the 20 biggest science fiction movers-and-shakers of 2008.