Here's my first post with some of my favourite classic books I thought a 12-year-old boy might like. Now here are a few more ideas from the comments that I really should have thought of myself:
The Dark is Rising series, by Susan Cooper: more well-loved British fantasy, with an Arthurian flavour.
The Blue Sword, by Robin McKinley: magic and swords and horses; what more do you want? One of my favourite books of all time. For a slightly older reader, I would say, but not because of anything inappropriate.
The Lemony Snickett books, for a slightly younger reader. I haven't actually read these, believe it or not, but I hear they're pretty funny, if you like your humour black.
The Chronicles of Ancient Darkness, by Michelle Paver: Stone Age setting and bonding with a baby wolf. Great story.
So You Want To Be A Wizard, by Diane Duane.* There are nine books so far in this series about two ordinary teens who stumble across wizardry and choose to take the Wizard's Oath to fight against the Lone Power. It's fantasy with a science-fictiony feel, because they get to go to other planets and meet aliens, and wizardry has lots of technical aspects (like temporal-spatial claudications). Great details like the spell to make your fridge door open into your friend's much better-stocked fridge. Plus cool philosophizing and amusing family members. I love these books.This was going to be the beginning of Part 2: more recent books, but it's getting late and this is already pretty long! Part 2 will be coming soon, I promise!
*I was intending to include this series in my post of contemporary choices, but indeed the books have been out for longer than my nephew has been alive, so they probably count as classics! They've just been released in new editions (as e-books, at any rate) that have been updated so the technology doesn't seem dated. (Am I feeling old right now? Heavens, no!)