Clark's buddy Pete Ross seemed to appear in every single scene, Lana had only two brief shots as a girl on the school bus making eyes at Clark and who was later identified in passing as "Lana." There were many references to characters from Superman's hometown, but one character who only got the briefest mention was Clark's first girlfriend, Lana Lang.
This is a clear nod to the character Chloe Sullivan in the TV series Smallville. In one of the teenage Clark Kent flashback scenes, where Jonathan Kent breaks up a conflict between Clark and bullies, a garage with the logo "Sullivan's" can be seen.There are also a bunch of Man of Steel Easter Eggs in Smallville as some of the businesses reference Superman lore, such as Ezra's Mail Depot, the Chloe Sullivan reference with Sullivan's Tractor Repair, and the Superman editor Mort Weisinger elementary school reference.
Also the mission code name for the invasion is "Trident". It is possible the the oil rig was taken down by Aquaman and the whales were signaling that Clark was okay.
So what secrets do those messages hold? Well, Snyder claims she can't remember, meaning you'll have to decode the alien language yourself to find out. However, "Man of Steel" producer Deborah Snyder revealed recently in an interview that they actually had linguists create a Kryptonian language so they could hide messages in Kryptonian. The computer displays in Zod's ship and the crashed seed ship display what appears to be gibberish in Kryptonian lettering.
Blaze Comics publishes Booster Gold's comic in the DC universe. During the final Zod battle, a logo for Blaze Comics can bee seen in the background.
So did Supergirl die 20,000 years ago? Or did she get back in her pod and emerge much more recently? Or was the lone survivor of the crash actually the Kryptonian serial killer? Looks like we'll have to wait for the sequel to find out. Unfortunately, a rogue killer murdered the rest of the crew in their stasis pods, but Supergirl herself apparently survived the attack - as hinted at by the one empty and open stasis chamber Clark finds when he enters the ship. It turns out that Superman's distant cousin (ancestor?) Kara Zor-El, better known as Supergirl, piloted that ship.