Towards the very end of Pandora (Season 9 Episode 9) when Chloe, Clark, and Oliver are in Watchtower Chloe puts her laptop on the desk. The cover of the laptop looks like an Eye- but if you look closer it's made up of the letters, J-L-A. Quite the foreshadowing.
The image that Lois sees in the future of Clark's shirt with the Superman logo on it, torn and blowing like a flag in the wind, is a reference to the Death of Superman comic, in which his torn cape is displayed the same way after having been killed by Doomsday.
This is the first episode of the season to have all the series regulars appear in the same scene.
In the future, General Zod addresses Clark as "The Son of Jor-El" before he super-kicks him. In Superman II, General Zod refers to Superman as "The Son Of Jor-El".
Zod refers to himself as "General" instead of "Major", the rank the original Zod would eventually attain on Krypton. In this case, it is likely a self-promotion as dictators often do.