my memory have betrayed me
quiet frankly the scenario you're talking about is quiet interesting yet
I havn't (or don't remmember) a manga with a story like this
take a look at this trope maybe you'll find a title that you'd like to read:
[url]http://tvtropes.org/pmwiki/pmwiki.php/Main/HumansAreTheRealMonsters[/url]

by the way In Ubel Blatt the main charachter literaly turn into a monster (if you consider a fairy as a monster) and start killing Humans (All humans who stand against him) and he is considered an enemy of Humanity (only a few Humans see his a a Hero) after being betrayed by his comrades when they were fighting the Witchtech (a Reptilian race)
by the way in one chapter in current timeline they showed an execution of Lizardmens and one of them was droping a tear (using libel "they were eating children", to make them scapegoat for a war that is intended as ladder for power-seizure)
maybe it hinted that Humans were the ones at fault taking into account all the scandals of the Empire see here

I just had a sudden brain wave and realised that King of thorns is pretty much what your looking for. Its got transformations and characters going over to the evil/monster side

About a girl thrown into a dystopian future where a virus has either transformed or wiped out all of mankind as far as the survivors of a cryogenic sleep can tell but the threat of the virus they went into cold sleep for is still imminent and to make it worse strange monsters are now roaming around the place. The virus changes type and becomes more of a transformation type as the story progresses and the main character has to come to terms with the monsters, transformed people and confront all the mysteries. The ending isnt siding with the monsters so to speak but she comes to accept them and does join up with a certain group of smarter ones

@Jaspery thanks for the link

@Tsubamex I'll definitely be reading that (I currently have about 10 tabs open with a bunch of manga I'll be reading from start to finish... Gotta stockpile them up in case I find myself with a shortage! :3)

Edit: I read King of Thorns... And added the Tragedy tag to it. That was pretty sad.

Bump

Maybe you should try the original Devilman (and all its derivatives)
Wolf Guy (the old and the new)
and Kiseijuu (you'll get when you read it)

I think this could be debatable, but in Seikai no Monshou (novel) the main character is an human and becomes an Abh. His father sold an human planet to the Abh empire in exchange of a noble status in the Abh society for him and his family. So in a certain sense we can say that he changes into an Abh, beside still being an human. But Abh are not what I'd call "monsters", from an evolutionary point of view they're superior to humans (think of them as space elves).
Story-wise, there is a war between Abh and humans, but I can say there are both neither good or evil, the Abh are mostly in war since they believe that humans are unable to organize themselves without making constant wars between them, so they're trying to subjugate them in order to guarantee universal peace and obviously the humans don't want to give up their freedom.
(I obviously simplified a lot the scenario)
I don't know if this can satisfy you, still I don't think there are many more stories which can fit better your requests.
For the material novel>anime>manga.

What I like in Trivial Pursuit style. Pick your category:[img]http://i379.photobucket.com/albums/oo233/Reid4891/Manga/trivia-1.jpg[/img]

Well, is not exactly a human turning into a non-human being, but is a human turning into something that is considered a monster between humans, in Trace (if you dont mind manhwas),

the second arc, where the mc sides with the "monsters".

In general the humans are pretty much the bad guys in this story.

Ganbare Seishuu! Ganbare Seishuu!

@jasperv I read Devilman and Kiseijuu already. And I've heard the ending to Wolf Guy is kind of bad... 🙁
@reid1 The story does look interesting... But they're hardly what I could call "monsters" or the like D:
@Raine-san Read Trace already too.

what about the other devil-mens manga like Neo-Devilman ?
Also Inugami (tought it has nothing to do with changing to monster) and Kurozuka
Dance in the Vampire Bund Well the seemingly human that turned into a monster was a werewolf with amnesia ... well forget the start its was just an excuse but the world of DiVB and the 3way underground war between fellow Vampires and Humans is a Good story