The place at the lake where Jor-El was buried is that same spot where the Kryptonian villains Ursa (Sarah Douglas), Non (Jack O'Halloran) and General Zod (Terence Stamp, who ironically does the voice of Jor-El in Smallville) enters earth in Superman II (1980).
The Kryptonian Council shown has the same setting of that of the Council from Superman 1978.
Zod tells Tess about the "bottled-up hopes and dreams of Kandor," which is likely a reference to the city being shrunk down by Brainiac and put in a bottle in the current comics. This also echoes a line said by Jor-El to Clark in Season Two's "Exodus".
The flashback scenes take place in 1966.
Curiously General Zod is not actually from Kandor. He was genetically made to be a soldier and tactician in defense of all Krypton. Supergirl (Kara Zor-El) is in fact one of the only survivors of Krypton who's from Kandor. Whereas Clark's (Kal-El) parents come from Argo city of Krypton.