I haven't seen a list of characters from the races, so for posterity here are the characters I saw.
Jingle Jungle 5k:
Mickey and Minnie (in green explorer clothes) before the start
Santa Goofy
Rafiki and Timon
King Louie and Baloo (in their parade outfits)
Chip and Dale (hats and scarves)
Donald Duck (snowflake outfit)
Pluto (Christmas hat and collar)
Overall it was a bit disappointing as there were no rare characters there; just the outfits from the parade.
Wine and Dine Half Marathon:
Chef Mickey (before race)
Chef Minnie (before race)
Chef Goofy (before race)
Chef Chip and Dale (before race)
Country Bears (Shaker, Liver Lips, Big Al, Wendell)
Main Street Electrical Parade Fairies
Main Street Electrical Parade Turtle and Bee (floats)
Rafiki
Flik
Timon
King Louie
Pluto
Jack Sparrow and Barbossa
Festival of the Lion King dancers
Green Army Man
Lilo and Stitch
Mr. and Mrs. Incredible
Darth Vader and Boba Fett
The Fantasia characters did not come out (although their location was there) due to the rain. None of the characters are unusual but Remy and Emile were greeting in France during the party after the run so that was a plus.
Characters do take breaks so there may have been others but these are the characters that I saw.