AstroGnostic: Revelations of the Matrix

The Matrix has any number of pop culture antecedents, but the most significant and by far the most well-known of them as far as the basic plot is concerned is 'The Cage' (aka 'The Menagerie'), the original Star Trek pilot that was reworked as a two-part episode during the original series' first season. 

We have three nearly-omnipotent figures with the power to alter a person's (specifically, an abductee's) perception of the physical world and do so while their subjects are imprisoned.

Slouching Towards Atlantis

Sometimes history converges in a way to kick our understanding of the world into a new plateau. Oftentimes it's not recognized until much later, but those with their ears low to the ground usually see it before others.

Christopher Nolan's Memento: The Mirror-Matrix

 

There’s a metatextual sequel to The Matrix that isn't recognized as such. The film in question features two of that blockbuster’s lead characters in prominent and analogous roles, and it tells much the same type of story that The Matrix does. 

Only in reverse.