While I enjoyed Toy Story 3, I absolutely loved the short film Day & Night that played in front of it.  It's the first film I've seen in 3D that effectively uses the technology for the purposes of the story instead of just spectacle.  For those who haven't seen it, Day & Night uses hand-drawn characters but inside the 2D lines are 3D events.  It's difficult to explain, but it basically uses 3D in a way that you've never seen before.  I'm not a big fan of 3D, but Day & Night makes a strong case that the technology can be an effective storytelling tool and not just a cheap gimmick that studios are using the combat piracy and jack up ticket prices.

Day & Night is now available to buy on iTunes.  Obviously, it doesn't have the 3D effect, but it's still a fantastic and imaginative film and I highly encourage you to check it out.  iTunes also has all of Pixar's other short films available for purchase.