An incredibly subtle one: when Jessie first meets Woody and realizes who he is, she excitedly exclaims "Sweet mother of Abraham Lincoln!" before running off to tell the other toys of his arrival. Woody's actor is a direct descendant of Abraham Lincoln via his mother, Nancy Hanks Lincoln.
Executive Meddling: When the decision was made to turn Toy Story 2 into a theatrical release while it was still in its early stages, Disney set a hard Thanksgiving release date — less than a year's time away, in an era when CG films took multiple years to complete — and told Pixar the date would not be moved regardless of their progress. When Pixar felt the story (and their staff) began to unravel under the pressure of the deadline, they had to convince John Lasseter, who was planning to take a break after a grueling number of years heading up Toy Story and A Bug's Life, to come in on short notice and help the team retool the film and get it out on time. The team were not only able to complete the film, but also churned out a film that more than held its own to the first; the meddling of Disney, though, helped kick-start the plan for the studio to operate independently, as well as dividing up their staff into smaller sections in order to not burn out their entire crew with each film.
Toy Story 2 could even be considered a trouble production. The project had started as a Direct-to-Video movie. Since the main Pixar team was wrapping up A Bug's Life, a smaller team at Pixar (which had made two Toy Story games) was assigned production duties. Though Steve Jobs later shut down Pixar's computer games division, the Toy Story 2 team was allowed to continue with the movie. When Disney executives saw the unfinished footage, they were so impressed that the movie got a green light to go to theaters. The problem was John Lasseter and others at Pixar weren't happy with what was already finished. As such, all the material for the direct-to-video movie was thrown out and the main Pixar team was brought in the finish the movie despite getting a nine month deadline from Disney on top of an exhausted and over-extended team.
What Could Have Been: Almost occurred, but thankfully averted. During the production of Toy Story 2, all the files from the film were accidentally deleted. Luckily, an employee happened to have a back-up copy of the work at home, rescuing what would have been two years' worth of work from oblivion.