The Sparrow (1996), by Mary Doria Russell
Everything you learned about first contact between humans and aliens was wrong. This strange and sad book chronicles what happens when the Catholic Church sends missionaries to a planet where astronomers have discovered life. The two species of aliens our protagonist priest meets are terrifying in their difference from humans -- and make the priest an alien to himself. Hauntingly written, this is literary science fiction at its best.

Newton's Wake (2004), by Ken MacLeod
From the first moments in this novel, when a group of Scottish organized criminals (erm I mean "combat archaeologists") jump through a wormhole with their "search engine" -- a giant machine for finding and pillaging cool treasure -- you'll be hooked. Funny, bizarre, and politically-savvy, this novel is about treasure hunters and rapture fuckers out to get a little cash and have a little revolution. You won't be able to forget it.