My favorite is probably Aurora, in which a generation ship makes a voyage to Tau Ceti to set up a colony.

After that, I really enjoyed Galeleo's Dream, a time-travel story about the famous polymath and a plot to reshape the history of scientific thought.

And Shaman is also great: it's about the paleolithic people who painted the chauvet cave and their struggle to thrive in an impossibly harsh time.

And finally I also just finished The Years of Rice and Salt recently, and it's one that I know I'll have to re-read sometime. It's an alternate history about how the world would shake out if the population of Europe was wiped out by a plague in the 1400s and follows a set of characters reincarnating over the centuries.