Hello Scott,
I think I have some great suggestions for your son. My oldest was nine years old last summer during our family trip to Walt Disney World and he enjoyed all of these. While these aren't necessarily "secret", they typically don't require waiting in a queue and are self-paced, so he can do as little or as much as he likes.
The first recommendation is
Sorcerers of the Magic Kingdom. This interactive game involves some trading cards, which are complimentary with park admission, a map and some good old fashioned fun. This was my son's favorite thing on our trip. It kept him interested while his little sister and brother enjoyed some of the smaller rides. No game is ever the same as it all depends on how you choose to use your cards. It is a great way to explore the parks and see some things you might not have noticed before.
Next, is heading over to explore Tom Sawyer Island at Magic Kingdom. Again, it is completely self-paced and it is a fun spot off the beaten path (in fact, you need to take a boat to get to it). One thing I love about this place is that the kids can run and play and explore while the parents sit for a bit to rest their weary feet. To get there, take the rafts from Frontierland. Keep in mind that this attraction closes at dusk.
My last suggestion would be DisneyQuest in Downtown Disney. Now, this place does require a separate admission ticket, but is included in the Water Park Fun and More add-on option, if you have that added to your Magic Your Way tickets. This is an interactive "virtual" theme park with several floors of attractions. Some of these areas may require a queue, so unlike the above two option, there could be some waiting involved.
I hope this offers some fun and enjoyable things to do that simply add more magic and fun to the magic of the parks.
~Allison L