Another one I just remembered (although probably unintentional) was Superman trying to catch up to the escape pod Lois was in and flying into the engine exhaust, and how much that looked like Reeve chasing after the rocket in STM.
I think we're missing one!
When General Swanwick gives the clearance word over the phone, he says:
"The word of the day is Trident."
Trident = Aquaman
Confirmed where? I'm glad though.
It was a hidden message. His weakness (or krytonite) was the environment of his home world. Sure, it's part of the story, but the fact that it wasn't blatantly called kryptonite makes it a hidden message and an Easter egg.
So Ive seen the movie twice now and caught only two easter eggs.
1- LexCorp logo on truck.
2- Wayne Enterprises Logo on the Satellite
What else is there?
Well the phantom Zone.
The scout spaceship was found in Canada, I'm assuming as an hommage to Joseph Shuster the co-creator of Superman who was canadian.
Also for those that didn't know, Joe Shuster also said Metropolis was modelled on Toronto and the Daily Planet was inspired by the Toronto Star Newspaper, which he delivered as a kid.