We always see:
Mickey & Minnie
Goofy
Pluto
Chip and Dale
Winnie the Pooh
Tigger
Eeyore
Woody (Frontierland and Paradise Pier)
Cruella de Vil
Alice
Peter Pan and Wendy
Lightning McQueen and Mater (They take turns at a meet and greet by the Cozy Cone Motel in Car's Land but they can't sign autographs for obvious reasons.)
Most of the time we also bump into:
Mary Poppins (Main Street)
Mike and Sulley (DCA)
Stitch (DCA)
Tweedle Dumb and Tweedle Dee
Buzz Lightyear
Jessie
Donald Duck (he had a meet and greet on the pier in DCA last summer)
Sometimes we see:
The Mad Hatter
Pinocchio
Evil Queen
Star Wars characters in Tomorrowland (clone troopers, Bobba Fett - Darth Vader and Darth Maul are part of the Jedi show but don't pose for pics)
Merida had a meet and greet area near IASW last summer. Don't know if that's still going. This summer there is a Frozen meet and greet.
In Pixie Hollow you can meet 2-3 fairies from the Tinkerbelle movies. Often Tink and one or two others.
Various Princesses are at the Princess area by the castle (forgot the name - I have teenage boys, so...)
We've seen:
Snow White
Cinderella
Belle
Sleeping Beauty
Ariel
Whatshername from Tangled
Tiana
Aladdin and Jasmine used to do meet and greets in Adventureland between the Tiki Room and the Jungle Cruise. Don't know if they still do that.
Rare sightings from the last few years:
Prince Charming
Prince Phillip
Fairy Godmother
Two girl mice from Cinderella
Queen of Hearts
Captain Hook (walking by - didn't know if he posed for pics)
The White Rabbit
I've never seen Piglet, but have seen pictures of other people with him.
When movies are released, those characters are often sighted. Over the last 9 years we've seen Mulan, Remi and Emile from Ratatouille, the kid and dog from Up (DCA), Brother Bear characters (DCA), the Incredibles, Hercules, etc.
Flik and Atta used to pose for pics after a show they performed in A Bugs Land, but that show is no longer. I'm not sure if they still appear.
You see tons of characters in the parades so keep your camera handy. They don't do autographs though. In parades and shows recently we've seen Phineas and Ferb, the Green Army Men, Dopey, Mr. Smee, characters from Three Caballeros...
When my kids were little we had a creative memories family autograph album. The pages could be moved around and I decorated with stickers after we got back, placing the photo of us with the character on the page opposite their autograph. Some of the characters got really fancy. The next year, our two kids each had their own, smaller book which I had pre-decorated with stickers. The signatures weren't as fancy and the pages couldn't be rearranged. It was hard to find the right page sometimes. I recommend decorating the pages afterwards, because you never know who you're going to bump into.
Have fun!