In Matt Phalen's graphic novel for middle grade readers, The Storm in the Barn, the Storm is real. It is a magical creature of terrifying power, an angry being that has been gathering its strength by withholding the rain from the parched lands around it. A young boy, bullied by his peers and dismissed as worthless by his father, becomes a true hero when he confronts the Storm and forces it to bring rain to the Dust Bowl. It's a great fantasy.
The Storm in the Barn (Candlewick Press, 2009) has just won the 2010 Scott O'Dell Award for Historical Fiction, that honors books for children or young adults (published and set in the Americas). It's the only winning book, since the first award was given in 1984, that's a graphic novel, and the first that's a fantasy. As Betsy notes at Fuse #8, this opens up interesting questions- "How much fantasy is allowed in a given book? How much history should be present?" she asks.
So I have quickly scrolled through the long list of books in my mind that combine history and fantasy (lots of time travel books, quite a few magic in the past books, lots of alternate history books that I don't count because they aren't real history). I've decided that it is fairly easy to tell if the history is there to provide backdrop and setting (a lovely example of this sort of book is Bewitching Season, by Marissa Doyle (my review), or if the fantasy is there to provide the reader with a way to engage with the history, one way of making "history" into "story." Many time travel stories, like the one I reviewed most recently--A Different Day, a Different Destiny, by Annette Laing (my review), do this.
I think it's pretty clear that The Storm in the Barn fits into my later category quite nicely. I would love to see books exemplifying this type of history/fantasy mix, where the history is privileged, winning future Scott O'Dell awards!
My own all-time favorite examples of solid historical fiction that is also a fantasy are Mary Stewart's books about Merlin, a series that begins with The Crystal Cave.
Viz the graphic novel side of things--here's Roger Sutton's take (and he was a judge) on whether a graphic novel should be eligible for a historical fiction prize.