The pillars where the Master and his wives sleeps is a real location.
The Master's "Lodge Of Sins" was actually the ranch of then El Paso County Judge, Colbert Coldwell. Sadly, the house where Manos was filmed burnt down. Hotel Torgo filmed the then abandoned house before it burnt down.
The scene at the beginning where the family pulls into a scenic overlook and talks about putting the top down was filmed on Scenic Drive in El Paso. It looks the same to this day. The city in the background that Joel calls "Beautiful Ground Zero" is Ciudad Juarez.*
Given the reputation that Ciudad Juarez has today, that riff becomes all that much more Hilarious in Hindsight.
According to the daughter of Hal P. Warren, his Halloween tradition was putting on the Master robe when he gave candy out. After her father died, her brother continued the tradition.
John Reynolds, who played Torgo, committed suicide about a month before the film was supposed to premiere. He badly hurt himself while filming due to wearing the satyr leg prop backwards, but his death appears to be unrelated to the film.
Jackey Neyman said in an interview that she had spent some time as a teenager and young adult looking for a copy of Manos in libraries and such, but never could find a copy. Then, one weekend in 1993, she received a call from her father. Apparently, he had settled in to snooze in front of the TV with Comedy Central on, and heard some familiar music during a certain episode of Mystery Science Theater 3000. Elated, she called Comedy Central in New York, told them that she'd been in this movie that they'd shown, and requested that she get a copy. The person on the other end was absolutely floored when she identified what movie.