Alas, Poor Villain: General Harmon in "The Seven Wonders Of The World Affair, Part II." Admittedly unlike most examples of his trope he doesn't get killed, but when he's exposed to the docility gas that he and the other bad guys plan to use in their scheme to take over the world and is permanently transformed from a dynamic man of action into someone who's one step up from a puppet - "Why don't you come out (of the elevator)?" "I have not been told to." - it's saddening. It helps that Leslie Nielsen, as Harmon, is the only cast member who actually made an effort in acting terms.
How about Captain Shark from The Shark Affair? He's a remarkably complex character whose aims are arguably quite noble, and when he refuses to let Napoleon help him get off his sinking ship at the end, it's actually pretty sad.
Badass Decay: Heroes Napoleon Solo and Illya Kuryakin are sometimes subject to plot dependent Badass Decay, when necessary. E.g., in the third act of the third season episode, "The Five Daughters Affair, Part II", Solo and Kuryakin fight THRUSH's "karate killers" (who despite that name (as given in the credits) do very little actual killing in the episode) for about the sixth time in this two-part adventure. Despite holding their own in several earlier fights with the karate killers, in this scene Solo and Kuryakin completely lose whatever fighting skills they've demonstrated earlier, and are straightaway handed their asses by the THRUSH "killers" in mere seconds. This is necessary, of course, to set up the fourth act's climax and resolution (therefore "plot dependent").
Complete Monster: Season 3's "Five Daughters Affair" two-parter (later released in theaters as The Karate Killers) has THRUSH agent Randolph, whose plot involves releasing seawater-derived gold onto the market in order to create massive profits for THRUSH. His actions include seducing the wife of the doctor who created the method then killing her once he has no more use for her, gleefully taunting her before murdering her; poisoning the doctor; attempting to behead Illya in an ice-chopping machine; smacking around Sandy; and shooting an unarmed elderly man just for raising his voice to him. These acts, coupled with his general Smug Snake demeanor, cement Randolph as probably the seriesís nastiest villain.
Fair for Its Day: Illya Kuryakin is not only a Russian, but a Soviet patriot and a commissioned officer in the Red Navy (at one point, he even appears in Soviet naval uniform). Still, he is never portrayed as anything other than a trustworthy ally and decent man. Not bad for a series first broadcast in 1964.
Not to mention the first episode shows the agency employing black and Asian employees; also they attempt to protect the leader of a new nation in Africa.
They Wasted a Perfectly Good Plot: "The Hula Doll Affair" features two brothers who happen to be rival THRUSH executives in a plot involving the title doll, which has a heat-sensitive explosive inside, and Napoleon impersonating a delegate from THRUSH Central. A recipe for power plays and suspense? It likely would be had it not been in season three and scripted by Stanford Sherman, who also did the one with Illya riding a bomb filled with essence of skunk ("The Super-Colossal Affair") and the one with popsicle bombs aimed at Victor Borge ("The Suburbia Affair"). Throw in the executives being played by Jan Murray and Pat Harrington, and their mother and real THRUSH Central member being played by perennial Large Ham Patsy Kelly, and... oh dear.
"The Five Daughters Affair", also from the third season, also applies, at least in regards to its cast. While Herbert Lom is utilized well, actors such as Telly Savalas, Terry-Thomas, Curd Jurgens and Joan Crawford are given small, unremarkable roles.
Woolseyism: The Latin American name of the series was translated as ''El agente de CIPOL" (The Agent of CIPOL), being CIPOL the Spanish acronym of " Comisión Internacional Para la Observancia de la Ley" (International Council for Law Enforcement). It also overlaps with Lucky Translation, as CIPOL sounds like the pormanteau for both Real Life agencies CIA and the Interpol.