Toy Story 3 was the first movie they made from start to finish knowing it would be in 3D. That said, it didn’t change how made the movie one bit. And remember, converting a computer animation film into 3D isn’t at all like converting live action. The end result of a “reverse engineered” computer animated movie has more or less the exact same result as one with it in mind from the start. You only notice a difference if you have gimmicky pop out gags like Dreamworks likes to do. Otherwise its all the same.
I would gladly repurchase the movie in 3D if I had a 3D tv, but I don’t think I’ll be able to afford one any time soon. I do have a 3DS though so I’m hoping we’ll start getting movies before long and that TS3 is one of the first ones to show up. It may only be be possible to watch it in 3D via netflix at first though.