Great topic, since Downtown Disney doesn't get a lot of love for its secrets ("subtle" isn't exactly in DTD's vocabulary). Some of my favorites:
1) The old train ticket booths for Pleasure Island are still there, but actually came from a train that used to circle the Fort Wilderness campground many, many years ago.
2) The Art of
Disney Store will let you purchase the old-style Magic Kingdom attraction posters (using print-on-demand). If you go into the shop and look up, you can see several of them arranged in a row along the highest wall, like your very own MK train station tunnel.
3) The carousel near Earl of Sandwich features several panels that show the Marketplace as it used to look, before some of the major overhauls (before McD's and the giant World of Disney store). I am especially fond of the panel that shows the kaleidoscope tower, which used to be in the area in front of Ghirardelli.
4) The handicap-accessible ramp in Pleasure Island has a sign labeling it Lombard Street. And if you look twice, you'll realize that it really does resemble a certain famous San Francisco road.
5) Not really in Downtown Disney proper, but Hotel Boulevard right next to it still has the original Walt Disney World Preview Center building (which still looks like it's straight out of the 70s). It's actually an office building now for an Amateur Athletics group, I think.
6) The pirate skeletons in the cages at the World of Disney (just inside the exit under the spitting Stitch) occasionally come to life (okay, this one isn't really a secret, but I still like them, and it's fun to watch the occasional kid get spooked).
7) Look closely at Fulton's Crab House, the Riverboat just past the T-Rex restaurant. You'll see that it's not a real boat at all, but it fooled me for years (of course, I was much younger then). Back when it was called the Empress Lily (named after Walt's wife), and it used to have smokestacks and a paddlewheel off the back that would actually churn, to help with the illusion.