Big Lipped Alligator Moment: 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 in purely to appease the actress, who was going to play one of the Master's wives until she broke her leg.
But Not Too Evil: Many people who watched the film were more than a little upset that Debbie was made part of the Master's harem at the end. While that is indeed creepy, the Master is bad guy, and a bad guy doing bad things is to be expected; doubly so considering he's a lunatic cult leader. Plus, you really should've seen it coming after the argument the Master's brides were having earlier in the movie.
Complete Monster: The Master is an undead occultist worshipping the evil god Manos who happily performs human sacrifices for his deity. He keeps a harem of wives which he disposes of as he sees fit, burning one alive after growing bored of her to appease Manos. When a small family is lured into his keep by his servant Torgo, he first kills the family dog. He tries to kill Torgo for touching his wives in their sleep, hacking off Torgo's hand in the process. He does this not because what Torgo did disgusts him, but because he considers them his alone. Then he forces both Michael's wife Margaret and his little daughter Debbie to become his new brides. He finally turns Michael himself into another brainless servant like Torgo before him to lure in more victims.
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 the 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.
And even when he does agree to leave, he still doesn't sound convinced that anything's wrong.
Harsher in Hindsight: According to some sources, John Reynolds (Torgo) permanently damaged his legs with the satyr prosthetics, and became addicted to painkillers until his suicide. Jackey Nayman, who played Debbie, claims this is just a rumor, though Reynolds did struggle with drugs.
Snark Bait: Its popularity is a clear case of this. It usually ranks high among the worst movies featured on MST3K. The RiffTrax remake of it was very highly anticipated; apparently, Manos was one of the most common requests for riffing.
Special Effect Failure: Torgo's knees, caused by the actor wearing the prosthetics backwards. He was nebulously intended to be a satyr. He wound up looking... like a guy with bulgy knees.
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.
Uncanny Valley: Debbie was dubbed over by someone who clearly wasn't a little girl. The result is more than a little off-putting.
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. He counts as a Jerkass Woobie as well, since he's a bit of a groper and a pervert towards Margaret.
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.