Why autographs? Well, it's not just the autograph... it's the photo opportunity too, and the interaction between child and character that all adds to the fun. The way Donald insists he is #1, how Goofy signs behind his head, how Chip signs his name and Dale's but writes "stinks" with an arrow pointing to Dale's name and then laughs. Just don't ask them if they are squirrels.
We did autograph books for my son when he was age 3 and again at age 4. We filled one book the first time.... and in 2009, we filled three books (sixty or so autographs!). We also had characters sign t-shirts and Disney baseball caps (clothing cannot be worn while being signed).
Autographs from "non-characters" and photos with them can be fun too -- the waiter, the chef, the bus driver, the bell hop at Tower of Terror, etc..
These are are favorite photos. Our son likes to show his pre-school friends where Pluto, Mickey, Lilo, and Stitch signed his shirt. He also looks at his autograph books and talks about the experience. We also made a photo book (shutterfly) that has these and other park photos with captions that tell a story. So, my son has his own hardcover story book called "My Trip to Disney World" with his name used as the main character. It all helps to preserve memories and build language skills.
I didn't see any long lines, the longest wait was about 20 minutes. Most of the time, less than 5 minutes... but we were at Disney during non-busy times of year.
Character meals are an easy place to meet characters and get autographs without waiting. In Animal Kingdom, the Mickey and Minnie greeting trail has several (almost no wait time) and also throughout the park and at the entrance. Hollywood Studios also had lots of characters and no or minimal waits - Animation Studios had several, also by Toy Story mania. The one place I have seen longer lines are for the Pooh characters by the Pooh ride in Magic Kingdom.