The scene of rain in metropolis after the main credits and before you see the limo is a recycled shot from Batman Begins (2005). In Batman Begins it is Gotham around the Arkham Asylum area.
Jimmy Olsen says to Chloe Sullivan that they could win a Pulitzer Prize with "your words and my pictures". Vicki Vale (Kim Basinger) says the same thing to Alexander Knox (Robert Wuhl) in Batman (1989).
Brainiac, the previous season's main villain, is referred to by his proper name for the first time.
Although it was suggested in "Perry" that Clark's powers were somehow related to the sun, this episode is the first in which it is verbally indicated (by Baern) that the abilities demonstrated by Clark and other Kryptonians are a direct result of their exposure to Earth's yellow sun.
The Crystal of El is a Kryptonian crystal shaped like the Kryptonian pentagon displaying the insignia of the House of El. This is also the iconic symbol 'S' of Superman.