Here are some updated places of where you will meet characters in my experience. My DS is a character junkie--he would be perfectly content to just character greet and ride the carrousel all day at DLR! So, I feel like I've become something of an expert on finding the characters. All of these are characters that we have met, not just ones that I have heard about other people meeting.
Fab 5/8 (if you include Daisy and the chipmunks!): Town Square early in the day and sometimes later (but not always) & in Toontown at opening--60 minutes after the rest of the park opens. One important thing to note is that Mickey usually doesn't have a PP photographer with him until he moves to the Barn. If that is important to you, wait until 2 hours after park open to go visit him. Pluto, Goofy, Mickey and Minnie are way easier to find that Donald and Daisy, with Daisy being the most rare. We ended up finally getting a picture with her during the character calvalcade parade that is part of MToTP this past October. Pluto is also the character that is most often at the second half of the Visa meet and greet at DCA. Chip n Dale are the characters there for the first half of the 90 minute meet n greet every morning from 10:30-12:00 by the Monster's Inc attraction at DCA. Pluto is also at Goofy's Kitchen (in a chef's hat for pictures at the door)and the Lilo and Stitch breakfast most days. A tropically dressed Minnie or Goofy (they take turns) also tend to be the door greeters at L&S most mornings.
100 Acre Woods: Pooh, Tigger and Eeyore are the most frequently encountered characters in the 100 foot wood greeting area in Critter Country. Piglet comes out once in a great while, but it is pretty rare to see him at DL. Typically Pooh and one other character are out at a single point in time, but if you are really lucky both Tigger & Eeyore will be out at the same time. Also, sometimes only Pooh has a PP photog, but if you ask very nicely you can get them to sometimes take PP pics of your group with Eeyore and/or Tigger.
Princesses: PFF (of course), Ariel's Grotto character meals, occasionally at Goofy's Kitchen, and sometimes out in front right after you come through the turnstiles, but before you go through the tunnel. We have met Cinderella, Sleeping Beauty, Ariel (in human form), Belle (in yellow dress and in blue dress), Pocahontas, Princess Minnie and Jasmine. We have also seen Mulan and Snow White at PFF but they left before it was our turn. Jasmine hangs out in Adventureland in a special meeting area by where the old Aladdin Storytime show used to be.
Playhouse Disney: We have met Annie, June (from the Little Einsteins) and Handy Manny outside the PHD theatre in DCA. We have yet to meet Quincy and Leo (also LE), but I have seen pictures of other people with them, so I know they exist.
Villains: Cruella Deville shows up by the Firehouse on Main Street and on the Backlot of DCA pretty regularly. She is the only villain we have encountered out on a regular basis, with the exception of Captain Hook, who is a regular at the Minnie & Friends character breakfast. However, during our Halloween trip this year at DCA we also met Hook on the Backlot, the Queen of Hearts (she scared my son silly!), and Lady Tremaine plus Anastasia & Drizella (otherwise known as the Evil Stepmother and Stepsisters from Cinderella). We saw Governror Radcliffe (Pocahontas), Bowler Hat Guy (Meet the Robinsons) and Frollo (Hunchback of Notre Dame), but did not wait in line to meet them. The Wicked Queen from Snow White also made frequent appearances in both normal and hag form outside of the Animation Building during the big Snow White celebration last year, but I have not seen her since.
Pixar: Sulley from Monster's Inc. and the Incredibles (Mr. & Mrs. plus Frozone) are also out on the Backlot quite often. Buzz Lightyear is found either outside of Innoventions or by the exit/handicap entrance for Space Mountain. We got pics/autograph with Woody by attending the Drawn to the Magic show at DCA.
Classic Characters: We met Peter Pan on the path going from where the fairies are now located into the castle. He was playing hide and seek and was super fun! We met Wendy standing next to the Carrousel in Fantasyland. While Alice and the Mad Hatter sometimes hang out by the AIW attractions, we have seen them more often out at the very front of the park, and both are frequent guests at Goofy's Kitchen. Mary Poppins and Bert are often visiting the piano player at the Coke Corner on Main Street, and we met one of the penguins at M&F.
Princes: The only one that we have met is Aladdin at the same spot that Jasmine hangs out at in Adventureland. Beast is occasionally seen at the Ariel breakfast, but we have yet to get that lucky! Other princes tend to only show up in the parades.
Lilo & Stitch: They host a breakfast at PPH and then are sometimes seen in the Sunshine Plaza at DCA.
Pixie Hollow: This is the newest character greeting spot and it is where you meet Tinkerbelle and some of her other fairy friends. I believe that there are a total of 6 different fairies, but only 1 or 2 others will be out with Tink at any given point in time. This area replaced the former Ariel meet and greet where you used to be able to meet mermaid form Ariel.
Random Characters: The Fairy Godmother is sometimes at M&F. Max (Goofy's son) is also sometimes seen at several of the breakfasts (we saw him at M&F and Goofy's). Baloo (Jungle Book) also visits Goofy's Kitchen. Meeko (Pocahontas), Koda & Kenai (Brother Bear) are the most common characters at the Chip n Dale breakfast at Storyteller's. We also met Gepetto at the M&F breakfast. Brer Bear and Brer Fox are out in Critter Country, either by the Hungry Bear restaurant entrance or the Splash Mountain exit nearly everyday.
Jack Sparrow: Used to hang out all over New Orleans Square and sometimes on the island, but as reported elsewhere, I have also been told that he is gone from the parks permanently (or at least there is no set return date at this time).
One final thing to note is that it can be fun to visit during different times of the year as many of the characters will change outfits with the season. The Fab 6, Pooh & friends and the Brer characters all have winter outfits, and the Fab 6 have Halloween costumes as well. We have also met Sorcerer Mickey, Tin Soldier Mickey, Vacation Mickey, Sailor Mickey & Goofy, etc.
We have filled 2 autograph books and are working on a third. I hope this helps and I would love to hear from others who have recent character sightings/locations to add to the list!