These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The entire subplot of the couple who keep getting harassed by the cops as they make out, which never comes close to having a point. It was put it purely to appease the actress, who was going to play one of the Master's wives until she broke her leg.
Designated Hero: Mike, who makes the disabled man carry their luggage in by himself after forcing him to let them stay the night at his house, and then has the nerve to complain about the state of living. Later, he orders Torgo to put the luggage back in car, "quickly" this time. There's also his stubborn indifference toward his wife's pleas to leave Hotel Manos, even after danger is made unarguably apparent.
His wife is worse since she openly states that she's okay with murdering him, and implies that she'd be OK with killing her own child if it was male.
Ear Worm: The only truly disturbing thing about this movie except maybe the ending is how thoroughly the haunting '"Torgo's Theme'" gets stuck in your head.
The ending theme "Forgetting You" (sung by the actress who played Margaret) is surprisingly catchy.
Hilarious in Hindsight: One reviewer◊ suggests that the film be repackaged or dubbed into becoming a "foreign art film". Warren himself is said to have remarked that it would make a great comedy if dubbed.
That same El Paso Herald-Post review snarkily referred to Torgo being apparently "massaged to death". 27 years later MST3K used almost the exact same joke ("they're Rolfing him to death!").
Snark Bait: Its popularity is a clear case of this. It usually ranks high among the worst movies featured on MST3K.
Special Effect Failure: Torgo's knees, caused by the actor wearing the prosthetics backwards. He was nebulously intended to be a satyr.
Squick: Specificially pedophilia and Torgo's creepy attempts to hit on Margaret. And that couch in the Master's living room, which the restoration showed was actually quite filthy and stained.
They Wasted a Perfectly Good Plot: Manos could have been really disturbing, if you look at the core plot or the idea behind them. You're lost in the desert, and the only person willing to take you and your family for the night is twitchy yet well-meaning, except when he randomly begs you to leave. It gets worse from there...
Made undeniably squickier by the fact that Debbie is the Master's daughter in Real Life. Ick.
Even the idea that the Master is only keeping Debbie to be his bride when she eventually comes of age is only marginally less Squicky.
It's all but directly stated that Torgo has raped or molested the Master's wives while they were "asleep," and that they were AWARE of this the whole time. Yet many consider Torgo to be the hero.
Vindicated by Cable: According to the Trivia, Manos actress Jackey Neyman herself couldn't track down a copy of it anywhere before MST3K aired the famous episode in 1993. Is it fair to say that Mystery Science Theater 3000 is the only reason the film is known today? Yes, it certainly is.
What an Idiot: Yes Mike, it's a good idea for you and your family to stay with the creepy bearded guy in the creepy lodge in the middle of nowhere. That'll definitely work out for you.
The Woobie: Due to his speech problems, hobbling gait, and the way Michael and The Master treat him like crap, Torgo manages to fall into this.
The Master's Wives are halfway there, with the implication being they are held against their will as the Master's sex slaves and there are hints that Torgo molests them during their hibernations. However, they appear to be extremely jealous and petty of each other and the new guests. Not to mention, killing Mike was their idea, not the Master's.