When my daughter was 3, she was scared of a lot more than I thought she would be. Of course, I remembered the rides from a teenager's point-of view! She was bawling in Mr. Toad's Wild Ride (scary part goes through hell with fire and devils), Snow White (the witch in the dark forest with lightning), and so we skipped Pinocchio (the whale is pretty intense). She wouldn't go on any coasters (she wasn't tall enough for most of them anyway). I almost convinced her to go on Matterhorn, glad I didn't! Its much faster, darker, scarier (the monster!) than I had remembered! We avoided Haunted Mansion and Splash Mountain altogether.
She got scared in the Honey I Shrunk the Audience 3-D movie (snakes and something else lunges out at you, air shoots up at your feet to feel like mice and bugs crawling on you).
There's really not any rides in ToonTown for little ones (crazy, I know), in fact, the only reason we ever go there is to see Mickey and Minnie. Other than that, there are 4 playhouses you can walk through, one coaster, and the RR ride (the line is never worth it). Its a nice place for a breather, but I wouldn't walk all the way back there if you don't have the time for it.
She loved Peter Pan (ya its dark, but you sit right next to mom and you fly!!), LOVED Dumbo, Its a Small World, Casey Jr Train, Storybook Canals, Carousel, Pirates (some parts were a lil scary, but overall she liked it and rode it more than once! It helps that it goes pretty slow and she can cuddle up right next to mom) Buzz Lightyear was super fun. Jungle Cruise, and Tarzan Treehouse was a HUGE hit, she played on there for hours. Very good spot to chill for a bit. The Shootin' Exposition is fun. Autopia, Teacups, and Winnie the Pooh (may not be worth the walk back there if they aren't particularly enamored with Pooh though)! Mark Twain Riverboat is fun, but the Sailing Ship Columbia is even better! You can go down into the boat and its all set up like a real ship, with pirate stuff. And they sail around Tom Sawyers Island and you can see lots of cool stuff hidden back there. Very fun!! Also, ride the train if you can...there are some very neat things hidden behind the scenes (dinosaurs!), and its great to relax and avoid the long lines in the afternoon.
At DCA, A Bugs Land is PERFECT for that age. Lots of little rides, lines not usually too bad. Also, King Tritons Carousel...she rode it 3 times in a row. Other than that, not too much to do in DCA for the little ones. (oh, toy story of course, they didn't have that when we went!)
And then the Star Wars Jedi Knight Training is cool!