That’s tricky! I would definitely say the first first (heh), but then I’m not so sure. I think the second one is a better overall film and is smoother, but while I think the third film is imperfect, it has so many interesting elements as well: two intense/moving scenes that I shouldn’t have to mention (especially the latter, which is a beautiful, quiet moment of simplicity—almost Miyazaki-like in style), some interesting uses of hue and lighting, and homages to cinema. I would consider the second Toy Story slightly blander in the visuals department (not ugly by any means—just ordinary), although there is a nostalgic, sepia look to some of the visuals, like Jesse’s back story.
I had to go with 1, 3 and 2 in that order. I liked the first movie the best, and the second movie was good too, but I liked Toy Story 3 a bit better than 2.