During the coliseum fight, the main characters from Final Fantasy 6 can be seen in the stands. From left to right: Locke, Mog, Relm, Strago, Terra and Umaro.

Many people believed that due to Square releasing Secret of Evermore, they never localized Seiken Densetsu 3 to the US. However, Secret of Evermore was actually developed by a new team hired in the US, many of whom had never worked in the industry before, and had nothing to do with the development of Seiken Densetsu 3.

It is widely considered that the lead hero is a reference to Marty McFly from the Back to the Future series. Both characters travel through time, use the term "heavy" and wear an orange life preserver. The lead hero also has a strong interest in movies, so this is possibly a development of that characteristic.

The soundtrack was composed by Jeremy Soule. While in Highschool, he played a lot of games and felt that soundtracks "lacked drama and intensity." He composed a demo to showcase what he believed music should sound like in games, and showed it to Square. They hired him as an in-house composer, and set him to work on Secret of Evermore as his first game.

The soundtrack was released on CD with 29 tracks, 8 of which were arranged versions of the in-game soundtrack. It was released as a pre-order bonus for the game.

In Ebon Keep, Cecil Harvey from Final Fantasy IV will appear as a store owner. Ebon Keep's theme on the official soundtrack is also called "Cecil's Town." He will even make reference to his adventures on the moon, becoming a paladin, and fighting Zeromus, hoping that the player will have heard of him.
If the player says that they do recognize him, he will give a discount.

The player can buy a Chocobo Egg on a market, a reference to the Final Fantasy series. Using it will boost the player's hit points.

In Omnitopia, the player's dog appears to be a robotic toaster-dog. If you remain stationary for a long period of time, toast will pop out of him.

The hero mentions a number of fictional films throughout the game, including "It Came from the Swamp" and "Mars Needs Lumberjacks". These are both obvious references to "It Came From Outter Space", and "Mars Needs Women".

Surprisingly, there is a third hidden message in the credits beyond Carltron's, "THE END?" and "DOLLY GRIP Brian Fehdrau," that reads, "It's Bill's fault." This message appears very briefly before the screen fades to black.

According to Fehdrau, the lead programmer, "It's Bill's fault" was an inside joke regarding Bill Kristiansen, another one of the programmers working on the game, who had "a particular habit of being at fault when [a build of the game] was busted."

If the player waits for approximately thirty minutes after "THE END?" is on screen, an additional message appears, stating, "You're a patient one, aren't you? Well, here's another cryptic credit, just for you..." Followed by the lone credit, "DOLLY GRIP Brian Fehdrau." This is a joke credit attributed to lead programmer, Brian Fehdrau.

Originally, the title for "Secret of Evermore" was simply, "Evermore." Squaresoft decided to add "Secret of" only a month before the game shipped, hoping that title familiarity with the already released Secret of Mana would benefit sales.

If the player waits for several minutes after "THE END" appears in the credits, an additional scene is shown wherein Professor Ruffleburg approaches a docile Carltron and says, "That's a good robot, Carltron. Dust, dust. Clean, clean. And no more plans for world domination, OK? Good." After Professor Ruffleburg leaves, Carltron turns to the camera with an evil grin. This is followed with a teasing, "THE END?"

In the starting town of Podunk, a "Doughead Software" store can be seen in the background. This appears to be a nod to both Egghead Software, a computer software retail company from 1984-2001, as well as the executive producer (and Lode Runner creator) Doug Smith.

Doug Smith may also be credited with the conception of Secret of Evermore, according to lead programmer Brian Fehdrau, who states that Squaresoft hired Smith based on his suggestion for an RPG with an "American-motif." Squaresoft liked this idea, and told the development team to make "a game like [Secret of Mana] with western themes."

If the player names their character "Fuck" (note that the name check is not case-sensitive), the skeleton in the desert will demand three Amulets of Annihilation to board his boat instead of the typical one, citing his distaste of foul language.

It's possible to acquire the dog's collars for free if you perform certain tasks or talk to certain NPCs while controlling the dog.

Leather Collar - Talk to Braveheart after defeating Thraax.
Spiky Collar - Talk to the Sting Alchemist in the desert after defeating Vigor.
Defender Collar - After being jailed for ruining the queen's banquet, defeat all the enemies as the dog before letting the boy out.
Spot's Collar - Talk to Braveheart after obtaining the Wind Walker.

If you defeat the Guardbots at the beginning of the game with no bazooka ammunition left, you'll see Carltron dusting some boxes in Crustacia as the protagonist washes up on the beach after defeating Magmar in Prehistoria.