They're also planning a sequel for How To Train Your Dragon, as well as a movie based off the Penguins of Madagascar TV series I believe. I don't think that the release Toy Story 3 has a lot to do these sequels, especially when this sequel for Happy Feet was announced a good year or two before Toy Story 3 came out, and that DreamWorks have released more sequels of compared to Pixar, as well as doing so more frequently.
Anyway, I'm not really sure where they could go from here for a sequel. While I wasn't impressed with Happy Feet, although part of that could have been due to the commercial breaks when it was airing on ABC Family, it did come to a satisfying conclusion that didn't open a lot of room for a sequel. Though, I guess that they just wanted to try for one after the first movie was so successful. I'm not sure if I'd go to theaters to watch it, but depending on what they do with the story and characters, I'd might rent it on DVD or wait for it to eventually air on TV.