I noticed and got sure about some things as well:
- The cars may not look different ("alternate universe/futuristic") but they don't emmit any fumes.
- SQUID appears both in the 3rd act, but you can see the acronyms in the small video conferencing monitor in Jon's lab, where the screen shows Veidt with a couple of scientists. Also, I may have a vivid imagination, but it seemed to me as if the teleportation energy around the last device was forming and moving in a tentaclish way...
- Not an observation, but since I had to watch the movie in a German movie theatre, the guy who dubs Tom Cruise was doing the voicework for Veidt

t:
- When Hooded Justice beats up Eddie, Night Owl I can be seen entering the room, right behind Silk Spectre I.
- Archie's thrusters are glowing blue. The small laser device Night Owl II is using in Karnak and Ozy destroys later leaves a blue spark. Nice little details pointing out how Dr. Manhattan changed the scientific appliances.
- I am sure that there are many more details
