The scene where Green Lantern is holding Supergirl after she's been knocked unconscious is a direct homage to the cover of "Crisis on Infinite Earths" #7, where Superman is holding the corpse of Supergirl.
In the comics, Supergirl and Brainiac 5 were actually a couple for many years!
Brainiac 5 and Bouncing Boy pass a wall of statues in the opening scene. On the far side, the statues are of Douglas Nolan, Ferro Lad, Saturn Girl, Cosmic Boy and Chameleon Boy.
The members of the Legion of Super Heroes who appear but do not speak include Chameleon Boy, Wildfire, Shadow Lass, Colossal Boy, Blok, and Timber Wolf. Additionally, images of (membership banner, l to r) Ultra Boy, Cosmic Boy, Saturn Girl, Colossal Boy, Lighting Lad, and Phantom Girl can be seen.
The robots Supergirl practices against are based on Blockbuster and Atomic Skull.