As Greg said above, Mechanical Engineering Design by Shigley is a great book.
However it is more of a textbook than a reference manual. (At Clarkson you use it for the Mechanics of Machine Elements course (MME). We refer to it as "the bible".)
If your son is just beginning his education, he will likely pick up a lot of these textbooks, or their counterparts as schooling progresses. So you probably shouldn't buy them for him now.
For reference manuals, you can't beat Mark's, Roark's, and The Machinery's Handbook. (as listed above)
Other gifts for the budding engineer:
Something else you may wish to consider:
Mechanisms and Mechanical Devices Sourcebook
Five Hundred and Seven Mechanical Movements
These two books, and others like them are fun for mechanical designers.
They show all kinds of cool things related to mechanical design.
If you've ever asked: "How do I convert constant rotary motion, into oscilatory linear motion with only mechanical components?" These books have an answer for you.
Another more costly set:
Ingenious Mechanisms for Designers & Inventors (4 book set)
This is a very interesting volume, of some of the same stuff as the above 2 mechanism books. Famously, one of these books is the "trigger" to open the secret passage into Dean Kamen's private quarters at Westwind. (Or at least it was at one point.)
Also consider, any book by
Henry Petroski. He has a couple really interesting ones, taking a look at topics such as design, and failure analysis. GREAT stuff.
Yes, I'm a dork.
JV