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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.
Foe Yay/Ho Yay: Blondie and Tuco, mostly carried through bizarre Does This Remind You of Anything? innuendo. They are really into tying each other up, Tuco bursts in on Blondie tenderly polishing his gun in his hotel room (not a euphemism), and while Blondie is talking to the naked Tuco in the bathtub, he smirks, while suggestively playing with the end of a bedpost. This is almost certainly intentional, as Sergio Leone made them share a bed for the whole of filming as Enforced Method Acting. Quentin Tarantino, who was heavily influenced by the film, claims to ship it a lot.
Moral Event Horizon: Angel Eyes crossed the line at the beginning of the movie, killing the son of the man he was hired to kill. It's one thing to kill the man himself, as that was just business ("When I'm paid, I always see the job through."); he didn't have to kill anyone else beyond those he was hired to kill (yes, those–just before dying, Stevens pays Angel Eyes to bump off the guy that sent him to do the deed).
The boy came running down the stairs behind him, rifle drawn. Angel Eyes was too smart to chance that the boy would be too scared to pull the trigger.
Tuco mentally torturing a dehydrated Blondie in a sunny desert. It's easily the character's most cruel moment. It makes Blondie finally gaining the upper hand by finding out the name on the grave that much more awesome.