The novels are listed by author, and then by publication (NOT necessarily in chronological order). The provided links bring you to a website describing the books or excerpts. I hope to one day make a page organizing the books by animal, but this will have to suffice for now (sorry)!
A ~ indicates a novel, while a * indicates a trilogy or series. NOTE: Some books have sequels, but if the sequels do not exceed two novels, they are classed as individuals.
AVI
*Tales from Dimwood Forest --- Mice
~ Poppy
~ Poppy and Rye
~ Ragweed
Adams, Richard
~ Watership Down --- Rabbits
~ The Plague Dogs --- Dogs
Baxter, Stephen
*Mammoth Trilogy
~ Silverhair
~ Longtusk
~ Icebones
Bell, Clare
*Pre-historic Cats Series
~ Ratha's Creature
~ Clan Ground
~ Ratha and Thistle-chaser
~ Ratha's Challenge
Clement-Davies, Davies
~ Fire Bringer --- Red Deer
~ The Sight --- Wolves
Graham, Kenneth
~ The Wind in the Willows --- Badgers, Otters, Toads, etc.
Hunter, Erin
*Warriors Series --- Cats
~ (1) Into the Wild
~ (2) Fire and Ice
~ (3) Forest of Secrets
~ (4) Rising Storm
~ (5) A Dangerous Path
~ (6) The Darkest Hour
Jacques, Brian
* Redwall Series --- Mice, Badgers, Squirrels, Hares, etc.
~ Redwall
~ Mattimeo
~ Martin the Warrior
~ Marlfox
~ Taggerung
~ Triss
~ Loamhedge
King, Gabriel
~ The Wild Road ---Cats
~ The Golden Cat --- Cats
Laskey, Kathryn
*Guardians of Ga’Hoole --- Owls
~ (1) The Capture
~ (2) The Journey
~ (3) The Rescue
~ (4) The Siege
~ (5)The Shattering
~ (6)The Burning
Naylor, Phyllis Reynolds
~ The Grand Escape --- Cats
~ The Healing of Texas Jake --- Cats
O’ Brien, Robert C.
~ Mrs. Frisbey and the Rats of NIMN --- Mice, Rats
Oppel, Kenneth
*Bat Trilogy
~ Sunwing
~ Firewing
Pierce, Meredith Ann
* Firebringer Trilogy --- Unicorns
~ Birth of the Firebringer
~ Dark Moon
~ The Son of Summer Stars
Williams, Tad
~ Tailchaser’s Song --- Cats