As fare as I can remember,Pixar is the only 3D animation company I know. But there has to be others right? Pixar cant be the only one taking all the awards for ‘best 3D movie’.
Well, there’s:
Blur Studios
Square/Enix
Disney (of course)
Dreamworks
ILM
To name a few 
I don’t know if they won any awards for best movie, but there is
Blue sky studios. They’re the ones who made Ice age and Robots.
also don’t forget Orange Studio
I didn’t wanna say Orange, because whilst it was a studio, I didn’t think it classed as a company. It was more of a project.
But it still deserves a solid mention here though. 
For…? 
Sony also has one, i forget the name, they are doing a movie with a bear, oh… my memory is bad, i saw a trailer in the movie theatre a whiles back.
You mean Open season? I also heard of others being done by warner bros.
Theres also Weta Digital and Lucas Arts divisions and whole bunch of others like that. Although they don’t usually make full CG movies, the CG special effects that add to real video is amazing.
hmm, sometimes disney works with pixar, but i dont think they specialize in 3d animation
also, square enix is a game company
Chicken Little and Dinosaur were done by Disney, without Pixar.
Yup. Disney are a 3D animation company, especially since they shut down pretty much all of their traditional 2D studios.
And Square/Enix is a game studio, but they did animate everything for Final Fantasy - Spirits Within. Also did the Animatrix short about the Osiris. So to me they count as a 3D company. (And a damn good one too!) 
It’s hard to know where to draw the line dividing studio’s from VFX labs etc.
Orange I agree deserve the title. Another one is Embassy FX, or VFX, I don’t remember which. They were the guys who did that nice dancing citroen advert in Modo.
There was a good interview with them somewhere online where they explained that they switched to Modo after the project had started. A brave step 
Yeah, know what ya mean. Since the thread asked for companies, I generally tried to exclude makeshift studios or visual effects houses.
Orange Studio, to me, wasn’t a company. It doesn’t have a trading name or even an actual corporate address. It was a short-term project to see if a viable studio could be constructed in order to produce a groundbreaking open-source film. And they succeeded. But unless they get permanent premises, funding, and potentially a steady income, I wouldn’t class it as a company.
I dunno. Perhaps pctopgs could let us know what they are looking for, being more specific. Should we list Visual Effects houses? Game studios etc…
Because if you start to include those, then the list gets an awful lot longer.
The Mill
Blizzard Entertainment
And then some…
Not to mention FFVII: Advent Children.