A single sprite of Lolo, the main character of the Adventures of Lolo series of games that were also made by Hal Laboratory, is hidden with the ship upgrade graphics in the ROM.

I don't know what those square eyeball-like things are that are floating above him, but I don't have much experience with or knowledge of the Lolo series.

As a matter of fact, Lolo sprites will take up extra space in memory whenever and wherever they're needed to.

Adventures of Lolo (NES)

HyperZone

Eggerland

The Egger enemy of HyperZone was very likely named after Hal's Eggerland series of games, of which Adventures of Lolo belongs to.

HyperZone Area 4

Kirby's Dream Land 3 Level 1

Kirby's Dream Land 3, also made by Hal Laboratory, shares three area titles with HyperZone. The first is "Grass Land", Level 4 in HZ, Level 1 in Kirby.

HyperZone Area 5

Kirby's Dream Land 3 Level 2

The second is "Ripple Field", Level 5 in HZ, Level 2 in Kirby.

HyperZone Final Area

Kirby's Dream Land 3 Level 6

The third is "Hyper Zone", the final level of both games. Seems like it's not coincidence and Hal was making intentional homages to their first-gen SNES title. Kirby's Dream Land 3 contains a plethora of references to other Nintendo games, so it's understandable that Hal would want to plant a few references to one of their own games.

   

The Box enemy has a Halken logo on it.

The microchip background seen in the ending sequence has "HAL" hidden throughout the gray sections of it.

Sound Effects #17 and #19 were reused in Arcana as sound effects for attacking enemies in the battles.

3D World Runner

HyperZone

Another NES game that utilized the 3D Glasses concept was Square's The 3D Battles of World Runner (or just 3D World Runner). Strangely enough, HyperZone's two segmented dragon bosses very closely resemble the segmented dragon bosses of 3D World Runner, especially the blue one.

F-Zero

HyperZone

HyperZone very strongly resembles another first-generation Super NES game, Nintendo's own F-Zero. The Mode 7 tracks look very similar and both have rows of lights for power recharging strips. The biggest difference is the mirrored track in HyperZone and, well, the fact that it's not a racing game like F-Zero, but a space shooter.

Space Harrier

HyperZone

Sega's Space Harrier is another game that resembles HyperZone and was the most likely source of inspiration for it, as well as 3D World Runner. The idea of the flying segmented dragon bosses originated in Space Harrier. Along with HyperZone's segmented dragon bosses, they also resemble the Mumoky enemies on the Grass Land stage.

Star Fox

HyperZone

Nintendo's Star Fox is another rail shooter with a behind-the-ship perspective on the SNES. But unlike HyperZone, Star Fox has true 3D polygonal models made possible by the Super FX chip technology. One particular part of Star Fox so heavily resembles HyperZone that it's almost hard to believe it's coincidence. On Level 2: Titania, the boss called Professor Hangar rolls along an overhead track overtop of a body of water. This looks very much like HyperZone's mirrored tracks, and especially the boss fight area of the Ripple Field stage, which is also over water.

Secret of Evermore

HyperZone

A minor coincidence, but the BM4 Reform ship looks like an old-fashioned pot belly wood stove. Square's Secret of Evermore featured an airship called the "Windwalker" that was powered by such a stove.

Tetris

HyperZone

The background of the Material Factory stage is composed of a grid pattern that very strongly resembles Tetrads from the popular, multi-console puzzle game, Tetris. This is easiest to notice during the ending sequence when the backgrounds are displayed normally instead of in Mode 7 view. Notice how each cluster of colors in the background is the exact pattern of a type of Tetrad.

Zanac

HyperZone

Compile's NES classic, Zanac, was also a shooter that contained a level (Area 6) with Tetrad-like patterns for the background.

HyperZone Box Art

Star Wars X-Wing

The box cover art of HyperZone was very clearly inspired by the Death Star battle from the movie, Star Wars Episode IV: A New Hope. The ship depicted on the HyperZone box resembles an X-Wing, which should be the first clue that something is weird because no ship in the game looks exactly like that. (The closest are the P-7 that you get in the Grass Land stage or the RW 91 that you get in Ripple Field, but neither are an exact match to an X-Wing.) Also, if you look closely enough, the pilot in the ship appears to be wearing a very similar orange-and-white uniform and helmet to that of Luke Skywalker in the movie. HyperZone's track is represented on the cover art as a "trench", not unlike that of the Death Star.

2001: A Space Odyssey

The entire game of HyperZone bears a strong resemblance to the "Star Gate" sequence in the 1968 Stanley Kubrick movie, 2001: A Space Odyssey. This may not even be coincidence, considering that Hal Laboratory was named after the HAL 9000 computer from that movie.

Those look like C 08 enemies.

Looks kind of like Ripple Field.

Blast Furnace?

This could almost be Grass Land.

HyperZone Final Boss

2001: A Space Odyssey Starchild

Also consider that the final boss of HyperZone is a giant alien fetus. It's like a corrupt version of the Starchild from 2001: A Space Odyssey.

(I honestly have never been able to decide what that is surrounding the final boss. Is it piloting a circular-shaped spaceship? Is it inside an egg or embryo? Is it just a weird glow with some odd fluctuations? If it is a Starchild reference, then the glow would make the most sense, but I'm just not sure.)