There's two different things coming out. There's a Toy Story 3 in development which is supposed to take place later in the life of the boy from the first two movies as he gets older and forgets about his toys creating an overall story arc for the three movies.
Then there's also what this thread is originally about which is a re-release of the first two movies, there is nothing being changed about them, they are just being shown in 3D. What this means is that it will still be the original two Toy Story movies but rendered stereoscopically so that it can be watched with those 3D glasses which all the 3D rendered movies are doing these days.
I'm sure the re-release is to refamiliarize everyone with the characters before releasing the third movie.