Paperman was fantastic and would probably be at the top of my list, but it's not a Pixar short it's actually under the Walt Disney Animations label. My favorite Pixar short would either be... Hmm, either Lifted or Partysaurus Rex.
Hmm, I think I liked the Day and Night one the most, even though I can only vaguely remember it. Though what I tend to notice even more is sense of confusion that runs through the audience when they realize "This isn't Toy Story/Cars/Finding Nemo/whatever" Clearly they don't know Pixar's habit of putting short animations as a little bonus before the main one. Some of the kids seemed to get impatient though
I really liked Paperman too. I saw it before Wreck it Ralph and I actually think I liked the short more than the movie. However, my personal favorite would probably have to be Presto. I thinks it's adorable and funny.