Gold kryptonite is seen for the first time. In the comics, gold kryptonite permanently strips Kryptonians of their powers, by destroying the ability of their cells to process solar energy. Smallville's version of the Gold-K causes injuries that Kryptonians cannot heal from, as shown by Clark Luthor (Ultraman) having a permanent scar.
Clark showed alternate Jonathan the shot gun that his grandfather had owned and recounts the story Jonathan had told to Clark Kent in Season Three's "Relic".
Luthor impersonates and lives Kent's life while on Earth-1 similar to how Bizarro lived Clark Kent's life with Lana in Season Seven's "Persona". Unlike Lana, Lois noticed something was wrong with "Clark" much earlier, however, Bizarro did make much more of an effort to pass himself off as the real Clark.
Clark Kent being pulled back to Earth-1 out of Earth-2 and screaming for alternate Jonathan is similar to how he screamed for Jonathan in Season Five's "Void" while being pulled out of limbo back into his native reality.
Clark Kent recited to Jonathan-2 what Jonathan-1 stated to Clark once before, "The only person who controls your destiny is you." in Season One's "Hourglass".