Oddities

Dialog Variants

• The dialog will differ a bit depending on Zohar's current form when you defeat him/her in stage 2-1.
• The after-battle dialog with Pablo will vary depending upon what you did during the battle.  The means to see all three variations follow.
  
• Defeat him in werewolf form without knocking the backdrop down
• Knock the backdrop down and defeat him in his human form
• Knock the backdrop down, but defeat him in werewolf when it gets put back up.
• The dialog after defeating Zohar in stage 3-7 will vary depending upon his/her current form when the battle ends.
• The dialog will differ in 6-4 depending upon Zohar's attribute and whether you defeated him/her in time or not.

Different Disks

Similar to what they'd done with Lunar: Silver Star Story on the Playstation, Working Designs released two versions of Silhouette Mirage with different disk art.  One disk depicts Megido, the other has Hal.

Vanguard Bandits Cameo

In a screen shot on page 24 of the manual, there is a green mech that is not seen in the game.  This mech is actually from another game called Vanguard Bandits, and was inserted by Working Designs as a joke.

Thanks to lordcyber for this bit.

US/Japan Differences

• The text, voice samples and ending song were translated to English (obviously).
  
• The code was rewritten slightly to allow the player to save the game to a memory card in either slot, rather than just slot 1.
• The memory card icon was animated.
  
• A completely new font was created for the English version of the game.
• Dual Shock controller support was added to the game.
• The "Options" and "Status" menus were added.
• All of the animations were re-mastered to look better.
• The Lunar 2 preview was added to the game.
• The Zohar mini-game was added to the credits roll.
• Super Core Fighter was added to the US version.
• The game was made tougher.  Parasite prices were raised, and enemy attacks do more damage.
• Using attacks did not cost Spirit in the Japanese version of the game, and you could not drain Spirit from enemies by using a same-attribute attack; it would simply lower their Spirit.
• There was a bug with the walker mini-boss in stage 2-2, where you would knock it off the back of the truck and it would not return to continue the fight, leaving you stuck there.
  
• The Japanese version's load screens are plain black screens with "Now Loading..." printed in the lower-left corner.
• The Reaper does not appear (Sega Saturn version only).
• There are numerous story differences, many changed to make the game's biblical references less evident.
  

There are many name changes between the two versions.  I don't have all of them at present, but here are the ones I know of.