The opening of the original Toy Story was totally ruined for the blu-ray release, imo. Pixar's version of the castle with Randy Newman's fanfare has been completely removed. I don't know how the second movie originally opened, but the new logos don't appear to have affected it as adversely. I wonder if there've been similar alterations to the openings of other pre-2006 Disney/Pixar movies like Bug's Life, Monsters Inc, Finding Nemo, Incredibles, etc.
Ratatouille, which is from 2007, uses a similar opening to Toy Story with the Pixar-lookin' castle. I guess that one made it to blu-ray unscathed because it was a new release and not catalogue.
Oh, and I love the irony of the touchstone logo on Nightmare Before Christmas being replaced by the Disney logo. At least they redid the opening credits to keep the score intact.
ETA: sorry if this post seemed kinda random. It was looking up the changes made to Lion King that got me thinking of Disney's own revisionism.