It can be a “If you loved this book, read this!” or just two titles that you think would go well together. Maybe it’s a historical novel and you’d like to get the real history by reading a nonfiction version of the story.
Lots of people love this question, but I have a really hard time with it. It may be that I'm not very imaginative. I was looking at my shelves, and it seems to me that a lot of the time, my tastes in fiction vs. non-fiction really don't overlap very much. I don't really care for historical fiction, though I love to read history. But Brona saved me, by pairing up books from her TBR shelf, and so I went and looked at my shelf and came up with a couple of things...
When the World Spoke French, by Marc Fumaroli, and Les Miserables, by Victor Hugo. I'm scared of French literature, but I do want to read both of these!
In the French vein, I did read two great books a while back: The Black Count, by Tom Reiss, and The Man in the Iron Mask, by Alexandre Dumas. Even better would be The Count of Monte Cristo, since it was inspired by Dumas' father's life.
Thames: the Biography, by Peter Ackroyd, and Our Mutual Friend, by Charles Dickens. Peter Ackroyd is just as long-winded and discursive as Dickens, and what's a Dickens novel without the Thames as a major character? From what I hear, Our Mutual Friend is a very Thamesy novel.
And it finally did occur to me that I read a nice pair just earlier this year. I've already wittered about Danubia, by Simon Winder, but it also inspired me to read a Polish epic poem, Pan Tadeusz, by Adam Mickiewicz. That was an excellent pair.