Can anybody answer since I don’t have access to my blu rays at the moment to check: Is it just Toy Story that is affected by the changed logo or is it all of those early PIXAR films as well?
As far as I know, the Toy Story logo plastering was done because the 3D version was a theatrical re-release so they had to add the new logo; also been told it’s because the original logo they did had no abilities to be put in 3D so they just decided to replace it.
Bug’s Life features the original logo; the 2009 Blu-ray; Ts2 was also re-released in 3D so I assume it has the new logo too. Monsters Inc, by myself I never kow if it had the new logo - probably the 2009 Blu-ray did had the old logo, but the 3D re-release may have the new. Finding Nemo is plastered (beacause it was also reworked in 3D and reissued to theatres), The Incredibles I think has the original logo, and Cars and Ratatouille, too.