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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.
Crazy Awesome: Special credit to Crazy Jane and Rhea post-transformation.
To put in special context with Rhea, she literally brought down a gigantic, levitating stone city which may have been a literal angel and helped put an eons long feud between two alien races to a halt simply because she got tired of waiting for Cliff's signal.
My Real Daddy: Even DC Comics agrees with this; their "Volume 1" trade paperback begins with Grant Morrison's run of Doom Patrol, at issue 19.
Fair for Its Day: Drake's portrayal of Rita Farr in the original series is surprisingly progressive, if still a bit dated to modern eyes.
Nightmare Fuel: The matter-of-factness of the art style makes the 1960s version of what Negative Man looked like under the bandages truly disturbing. Grant Morrison's run quite deliberately injected quite a lot of horror imagery.
The Candlemaker. Sweet Jesus, the Candlemaker.
The entire arc with the Scissormen, especially when they first start to breach reality.
Some Anvils Need to Be Dropped: While some argue that Coagula from Rachel Pollack's run was a Mary Sue, the fact of the matter was that were virtually no other positive representations of transgender characters in superhero comic books at the timenote hell, there still isn't, so it's no wonder that Pollack strove to create a strong and competent transsexual superheroine.
Tough Act to Follow: Morrison again. The strong Pollack and Arcudi runs often suffer unfairly in comparison, since Morrison's is regarded as one the very best superhero comics of the late 80s/early 90s.
In the 1960s, version the characters are all viewed as "freaks," including the Chief... because he uses a wheelchair. Fortunately, attitudes towards disabilities have changed somewhat since then.
When it turned out Monsieur Mallah and the Brain were in love, the reaction of most people was "OMG, they're gay! That's disgusting!" Never mind the fact that one's an ape and the other a brain in a jar, it's the fact that they're the same gender that they found offensive.