I saw Toy Story 3 in 3D and really enjoyed it. I think the effect works well for these computer animated movies. Although, it's a strong movie either way, so I'm sure it can be enjoyed in 2D just as well.
When deciding to see a movie in 2D or 3D, one factor I consider is - was it filmed natively in 3D, or converted after the fact?
Before I was aware of the difference, I saw a few movies in 3D.... to me, "Coraline" and "Avatar" looked great in three dimensions. Realistic and not distracting. But "Alice in Wonderland" and "Clash of the Titans" looked somehow....
off. Rather "flat" with 3D cutout effects that seemed to distract me.
Turns out, the 2D source footage for those latter two movies was converted in a computer after the fact, rather than being filmed with dual cameras originally (or rendered with two "virtual" cameras in the case of a computer animated film).
So for the record, Toy Story 3 was rendered in true 3D, if this issue is something you want to go by. Here's a handy list of movies separating the real 3D films that were shot/rendered natively in 3D from the fake ones that weren't:
http://realorfake3d.com/
And here's an article about true 3D vs. "fake 3D"...
Michael Bay And James Cameron Skeptical Of 3D Conversions: "The Jury Is Out"