Board games: thought-provoking, social, fun, and absorbing, probably not what you remember from your childhood anymore.
Some suggestions:
Settlers of Catan
Nexus Ops
More general audience:
Apples to Apples
Classic:
Diplomacy
Impossibly deep and ancient:
Go
Heck, back in my day (high school in the '80s, College in the early '90s) bringing knives to school was a non-issue, i’d spend many a HS study hall idly flipping the tools open and closed on my Swisschamp, i had a cheap butterfly knife i used to flip open and closed while sitting in the community lounge in the dorm wathing TV, nobody batted an eye, nobody ran whining to the R.A…
He does have a copy of The (New) Way Things Work, right? It’s a must for any kid.
Other good books at his age are Eregon , anything by Eion Colfer and The Immortals series by Tamora Pierce. My son was not a willing reader until he read these books at about 12 years old. Now he’s a voracious reader.
But a pocketknife’s a good idea, too. It’s sort of a rite-of-passage present. No one would give a little kid a knife, right? WhyKid’s got several. His favorite is his Leatherman.
Hmmm. Eragon I assume you mean? Well, let’s put it this way, I’m pretty sure the writing won’t be beyond his reading comprehension level 
Yes, and don’t be snarky. It has a reading level of 12+ and a read aloud level of 10+.
When your kid won’t willingly read a thing, you’re happy when he picks up the cereal box.
Any (or many) of the Larry Gonick “Cartoon History…” or “Cartoon Guide…” books on history (includes natural science) or the various disciplines of physics, chemistry, genetics, statistics, etc.
(A good snake would not be an issue with the cats or rabbit (provided you got a good cage). I would avoid the smaller corn snakes as they are world class escape artisits, but a medium sized ball python would probably be OK. DO NOT get an iguana, of course.)
I think the very best thing you can give a kid that age is you. Take him camping or fishing. Go on a weekend trip to somewhere you can both enjoy. Get him a remote controlled airplane and go w/ him to learn how to fly it. Get two, or three, pairs of rollerblades and use them regularly w/ him. He’s about to enter the toughest period of his life, stay involved and let him grow up, but w/ your guidance.
Well, then the obvious choice is an accordion.
However if you would like to maintain your sanity, the Discovery Channel Store has some really cool stuff, especially for those with a scientific/nerdy mind.
MAGNETS!!! I don’t know any kid who wouldn’t be happy to play with a bunch of magnets and various magnetic thingies. My son (younger than yours) loves magnets, but I gotta say, Dad and I have at least as much fun with them (OK, I have more fun with magnets than anyone else).
If you have an “educational” type store conveniently located, you can pick up all sorts of magnet stuff, including little vials of iron filings and little lumps of iron, etc. to drag around with the magnets.
As far as boardgames go, I found a great one called Blokus. Seriously good for any age. My 8 year old is ruthless at Blokus. Way better with 3-4 players than with just 2.
How about a chess set? Maybe a little “man kit” with some deodorant, some of that body spray stuff, some nice minty chewing gum…you know, guy stuff. You could put it all, gift basket style, into a little tool box or tackle box, or some other manly sort of container. Let him know that even though he’s your baby, you know he’s no baby 
My favorite part of my birthdays as a kid was that my mom would take me to “grown-up” restaurants and not even advise about the menu (now, we’re talking about a woman who raised 9 kids on her own, and she was far from worldly). If I wanted chicken fingers, that was OK. If I wanted steak au poive, that was OK too.
Happy Birthday to your young man!
Word.
Cartooniverse
When I was 12 or 13 my mom gave me for my birthday Karate lessons. One of the best gifts I ever got. What I learned mentally and physically has stuck with me my whole life and helped make me more well-rounded and confidant. Plus you get to hit other people, and it’s OK.
Me too, my friend. Me too.
Double word.
Cluricaun. 
Word to the third!
When my son turned 12 he got cooking lessons from me. He’d get to pick out what he wanted to make, we shopped and figured it out together. He’s turned in to a right good cook, too!
And if you combine that with:
I think that would make a really COOL gift.
I’d ask my son what he thinks, but he’s at school and always says MONEY anyway.
thank you for all the wonderful suggestions!
Missy2U, Hallboy has been cooking for about two years now and he frequently helps out in the kitchen when I’m fixing meals. Last weekend, he had a friend spend the night and the next morning Hallboy made Lemon Poppyseed Muffins. He makes his breakfast every morning (this morning it was an egg burrito) and will help me plan meals if I push it.
WishIHadACoolName, he’s been well aquainted with deodorant for about a year now. (Kids are maturing a lot faster than they did when I was a kid!) Ever smelled an eleven year old male after track practice who wasn’t wearing deodorant? It could be lethal to give them a ride home! And, since his appetite outranked mine a few years ago (and he began to eat the food off of MY plate), he’s not ordered off the kiddie menu in some time.–I swear, this kid will be taller than I am this time next year.
Although I think there are so wonderful ideas in this thread, A.R. Cane, I think you hit the nail on the head. We used to do quite a bit of camping when Hallgirls were home, but since they’ve moved out on their own, we’ve let that slack off. Last week, Hallboy and I went canoeing, and I think the weather will be warm enough for us to spend the weekend camping. I’ll look up the campground reservations while I’m thinking of it.
As a magaine junkie myself, parsnip, I took your advice and bought Hallboy not one, not two, but THREE magazine subscriptions for his birthday. He may not be thrilled when he opens the package with the gift certificates (and maybe I’ll go and get a copy of the magazines at the bookstore if I can find them), but I know for a fact that he’ll enjoy them every month that one arrives in the mail.
Of course, the advice in this thread has already pushed me into action for thinking about Christmas…
Are you guys into hiking while you’re camping? A walking stick is a treat to have while walking in the woods. It feels good, it’s good for show, and also to whack at small branches, which every kid loves.
12 is old enough to start learning how to tend the campfire, as well. Leather welder’s gloves are good for protecting your hands from bark and fire.
I’m glad you figured out what to get your son for his birthday, phall0106. Here are some ideas for Christmas:
Is he familiar with Dr. Demento? How about Tom Lehrer? Firesign Theatre? A Dr. Demento compilation might be a fun gift. Some “best of” Tom Lehrer might be a good choice, too. How about Give Me Immortality or Give Me Death, by the Firesign Theatre?
Does he have a microscope? I had a microscope as a kid, and it was one of my favorite toys. Stayed that way for years, too. You could get him a field microscope and a good, strong flashlight for looking at cool stuff he comes across while he’s outside. He could carry the field scope and flashlight with him and go on walks. Then he could check out a very close-up view of almost anything he comes across. That’s a great thing to be able to do no matter where you live, in a city or otherwise.
D & D gets my vote.