I'll try to be unique here and give you a few that aren't talked about as much but with a few qualifiers.
100 Cupboards: (I've only finished the first book, but I like it. The writing style is a bit more challenging and abstract than most YA fiction is. It isn't written like most things for kids are written, but I remember it working beautifully)
The Edge Chronicles: (Dry reading at times due to uninteresting main characters and formulaic prose style. Varies greatly in actual entertainment value from book to book. The "Twig Trilogy," the first one written, is the only one entertaining through all three books. The fantasy world created by Stuart and Riddell is one of the most unique on the market though and presents unique story opportunities. The countless ink illustrations bring it to life. If your child likes worldbuilding he'll enjoy it for that alone. Works great for kids who liked Dr. Suess when very young and want to see that same weird cartoonish imagination applied to something more grounded and grittier as they get a bit older. I only read up to "The Immortals" when I was younger because that was the planned ending. They've made more three more books since that though)
The Mysterious Benedict Society: (I read the first book and got a kick out of it. I liked the characters, the unique story, and the twists it took. I didn't like the second one as much because it followed sort of a National Treasure/Indiana Jones/TinTin kind of story formula which didn't feel as fresh or interesting to me at the time. Somebody tell me if the books following that were any better. I haven't read them)
The 13th Reality (I've only read the first two of these, but I liked them enough. They aren't masterpieces but they've got some good brain-tickling ideas in them. If you like "Beyonders" you may like these. They're similar in some ways)
The "Secret" series (The books that start with "The Name of this Book is a Secret): (I got a kick out of these at the time but in retrospect, it's more obvious to me that they were borrowing heavily from "A Series of Unfortunate Events" and doing it too soon. That's not to say it's a rip-off, exactly. It isn't as meanspirited or formulaic as ASOFUE, at least, so may serve as a substitute if you prefer things that way)
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Cherub series for M15 kid spies addressing real world problems.
Skulduggery Pleasant series for magic mischief and a skeleton detective.
Magic fantasy and medieval setting with kickass female characters, anything by Tamora Pierce.
Horse's, adventure and mystery, the Black Stallion series.
Adventures with a male character in a medieval setting, Ranger's Apprentice series.
The Guardians of Time series, about time travel and history.
Maximum Ride series - its edge of your seat.
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Boxcar Children (LOVED these when I was a kid), Series of Unfortunate Events, Nancy Drew, Hardy Boys, Magic Tree House series (this was the series that inspired me to read), Eragon, Amelia Bedelia (for beginning readers)