The code Luthor enters "060669" refers to June 6, 1969, the day the Kinney National Company bought out Warner Brothers Seven Arts. Kinney National had previously absorbed both DC and All American Comics in 1967 so this day is effectively the day DC comics merged with Warner Brothers; essentially making the WB DCAU possible.
This episode is different from others in that it focuses on the efforts of the villains. In fact, we do not see any members of the Justice League (specifically Green Lantern, Batman, Atom-Smasher, Captain Atom, Superman, S.T.R.I.P.E., Red Tornado, Orion, Dr. Fate) until the very end, and they have non-speaking roles.
The original recordings of Tala's screams were found to be extremely disturbing by The show-runners, so they were decreased. However, they still found the ones eventually used to be unnerving.
Toyman's line of "We're heeereee" mimics the classic line of "They're heeeerreee" from "Poltergeist".
The song that Toyman hums to himself is "Mary Had A Little Lamb".