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do cartoon characters count if they are anthropomorphized animals?

Well, there's already Superfrog and probably others which are marked with this tag.
There's also the barely used anthropomorphism tag group to mark games with them.

These are border cases and there's no way to differentiate real animals from cartoon anthro animals currently (like aforementioned Superfrog, or Mickey Mouse and others).

Perhaps introduce anthropomorphic protagonist and exclude anthropomorphic objects and machines from it. Funny animal is the other name for them, but I think that ties too closely with comedy to work as a generic name.

Edit: "anthropomorphic animal protagonist" would automatically exclude the other cases, but I think the name is a bit too long :)

Agree to not include anthropomorphic animals here, I'm more curious about "looking real" animal protagonists.

I guess its a question of 'realness' within the fiction supported by minimal suspension of disbelief. I don't think Mickey Mouse is actually counts as a mouse, he interacts with his world as if he were human and the other characters in that world treat him likewise. As opposed to Bambi who is still a deer, despite being able to be heard by the audience in their own language and reacting with human like emotions and having a few other behavioral abnormalities for a deer (such as monogamy). The mouse in the movie Mouse Hunt is a mouse. The rats in Secret of Nimh would be a tough call, the normal rats and mice they interact with would be considered animals (with some suspension of disbelief), but the rats themselves state "We can no longer live as rats", claiming non-animal status for themselves and willingness to risk their entire existence to backup this claim. I would agree that they are no longer animals simple because of their claim and successful defense of it. Another tough call is the toys in the movie Toy Story. Again the deciding factor for me would be what the Toys decide about themselves. They claim not to be alive and are only capable of feeling alive when they are being played with. However, some of the toys attempt to claim autonomy. Buzz believes himself to be an actual living space ranger. This claim turns out to be a delusion and Buzz accepts his existence as a toy. Despite being capable of movement and apparently able to make decisions, he is still an objectprotagonist (or whatever term was decided on for animate objects). Woody attempts to choose the path of his life as if he is a freewilled living individual by agreeing to the prospector's plan to be 'immortalized' in a museum. Whether this plan will work or is just another vain delusion turns out to be a mute point; in the end he agrees he is Andy's toy and denies any claims to the contrary. The prospector has no delusions about being a toy and is quite angry about it. He's decided to be a toy on his own terms and only accept owners from behind safety glass and security systems, rather than fulfilling the traditional toy role of being played with. He selfishly wants joy without having to give any in return. Being able carry out this plan might have actually proven his status and an autonomous being. But in the end, he is forced to be a toy against his will. To sum up, they are all toys because they are unwilling or unable to act otherwise, and this isn't necessarily a bad thing. Number 5 in the move Short Circut claims to be a living being in a most pointed way. He understands death and wants to avoid his own. He understands death well enough to realize the hypocrisy of killing other living beings to save his own life. In fact, he sees the death of any living being as equal to his own. This is not morality, as he has no idea between right and wrong (though he learns the difference later in life); he didn't even understand death until after he had killed a living creature. He has no qualms with destruction of non-living objects, including his four non-living 'brothers' and an identical non-living duplicate of himself that he constructed. He is able to successfully defend his life, and claim personhood, and eventually able to achieve legal recognition of both in the world in which he lives. One last question; are there animal antagonists in Alice in Wonderland? Alice is definitely the protagonist, but ultimately she is also the antagonist, since all the antagonists are from her own mind. But does this count?

So it is still a question of 'realness' within the fiction supported by suspension of disbelief and by the characters willingness and ability to successfully defend their own beliefs about their nature. Its simple, we need to ask the protagonists, "Who are you? Explain yourself."

Ōkami has a "human" goddess born as wolf or some such, and I think animal protagonist works quite well in that, even though it would be by her inner judgement to be completely wrong :)

Does she successfully defend her position? Must she interact with her world as an animal or a human goddess?

Here's one to think about. Is there an animal protagonist in Twilight Princess? I say yes, because while a wolf, Link cannot open doors, talk to people, or use a bow, sword, or fishing pole. He must interact with the world as a wolf.

Well, I added the new group and changed as many instances as I could recognize to use it. The specific animal type (mouse, bird, felid, etc.) tags should apply to both animal protagonist and anthro protagonist tags though, so they shouldn't be removed from anthro instances.

Edit: Also edited the first post in this thread so it's visible in the group page. Makes the thread a bit confusing now, but group articles aren't very good places for discussing these anyway :)