Trace decay is the theory that memory leaves some type of trace, a physical or chemical change, within the brain that begins to decay over time.
The piano in the Mariposa plays "House of the Rising Sun" and Amy Winehouse's "Back to Black".
Ford's quote "One man's life or death were but a small price to pay...." is a direct quote from Mary Shelley's Frankenstein.
The area where William and Dolores come across the framework of a church steeple has a unique rock formation behind it. This is the same natural rock formation that Kirk fought the Gorn on in Star Trek (1966). It is called the Vasquez Rocks and is located in a Nature Park near Los Angeles, California.