In The Triplets of Belleville (2003), when Madame Souza arrives at the triplets' flat, the turd floating in the toilet bowl is shaped like Mickey Mouse
In Shin Godzilla (2016), there is a very brief moment during a Twitter sequence where you can spot a profile called @bakashinji with an Asuka Langley profile pic. The director of this film, Hideaki Anno, also directed Neon Genesis Evangelion (1995)
When The Oneders play at The Orpheum theater one of the other acts on the marquee is Marilyn Lovell and The Geminis, a reference to Tom Hanks earlier film, Apollo 13