1) Little Pea, Little Hoot, and Little Oink, in their respective books.
2) The Runaway Bunny
3) Wodney Wat (although Camilla Capybara is cool)
4) Tacky the Penguin
5) Zorro the Dog
6) The Little Skyscraper
7) The Pigeon
8) Most of Eric Carle's animals
9) Thing One and Thing Two
10) The Mouse that you may or may not provide with a cookie
11) Scaredy Squirrel
13) Most of Leo Lionni's characters
15) Harry the Dirty Dog
16) Rainbow Fish
At least there's Mike Mulligan's steam shovel.
This will be followed by a list of animals that are probably assumed to be boys but totally don't have to be. Add to this list in the comments!