Skull Gem is a type of gem that was scrapped from Bejeweled Twist. It has no graphics and instead appears as a bare space on the board. Using a hex editor, you can make Skull Gems appear on the board. 
In the Spanish version of Bejeweled Twist, Skull Gems and Doom Gems share the same name.
According to evidence found inside the game files, it appears the Skull Gem would have appeared after Level 24 in Classic Mode. If this setting is changed, the game will freeze before it gets to the main menu.
If the Skull Gem reaches the bottom of the board, the game ends and the game crashes.
The message when the Skull Gem first appears shows "What's this? This SKULL is chomping thru your gems! Destroy it before it hits the bottom!" and "If the Skull reaches the bottom, it will destroy one of your Shards!"
It's possible that "Shards" is a scrapped mechanic, possibly for a mini game.