The unseen, mysterious force rarely referred to in Chrono Trigger known as The Entity is parallel to Jehovah, the God of the Bible.
In the Bible, Jehovah rarely interacts with his creation. He mostly either watches or subtly guides individuals through feelings, dreams, or visions. This is similar to The Entity in Chrono Trigger, never really showing itself definitely, but being more of a mysterious force that makes itself known only through feelings and emotions.
Notice that in the end of the game, some of the characters who had the conversation about The Entity beforehand say that they feel The Entity is satisfied at what has happened. The time gates disappear, showing that they may have been a bit of help from The Entity. This further enforces the similarity to Jehovah, who dosen't really interact in major ways with mankind, but rather through more subtle methods, and only on rare occasion.
There is a Biblical story in which Jesus travels out into the middle of the desert, and speaks with God. Similarly, in Chrono Trigger, the first time Crono's (Jesus's) party seems to notice and discuss The Entity is when they are in the area that was once a gigantic desert (Fiona's Villa).
Since Jesus Christ was the son of Jehovah, this leads one to hypothesize that perhaps The Entity is the true father of Crono (Jesus). Notice that it is a gigantic mystery as to who Crono's (Jesus's) true father is in the game. Not once is his father mentioned.
Near the end of Chrono Trigger, it is mentioned that The Entity, the mysterious force that seemed to drive all of the past events to an extent, may have wanted the characters to witness all of it. This can, in a way, be interpreted as an allusion to The Entity actually being the player of the game, in that the player is the one who truly controls all the actions of the characters and whether or not they succeed in their quest. This sort of places the player as sort of a God figure, having omniscient control over the game. This again reinforces the strong similarity between The Entity and an all-powerful God. Thanks to Shawn Williamson (CloudSW@aol.com) for this piece of information.