I can think of quite a few. First, do femme fatale characters count? White Heat's Verna predictably escapes unscathed in a comic relief moment. Con Air has some transgender comic relief surviving whilst Cyrus the Virus dies. In a classic yet not as condescending example; Even though she does end up dying later, Irma Vep out of Les Vampires outlives all three of her head vampire bosses.
In another silent film; Dr. Mabuse's henchmen (From "The Gambler") outlive the titular doctor, at least where sanity is concerned. (I guess this doesn't count at all though since the remaining men both seemed to be quite suicidal following their defeat
)
How about the giant octopus/gate guardian thing in hellboy? Surely Rasputin was the main villain even though the guard was more powerful.
Two of "The Three Storms" out of Big Trouble in Little China I believe fall into that category that you hate, reappearing after the main baddie dies as another challenge (Unless you meant the "not quite dead" cliche where they actually seem to die before coming back).
The crawling hand in Waxwork returns in the sequel, though we already see it lived in the original I find it happily amusing that Anthony Hickox actually followed through on his original "sequel window" instead of ignoring all continuity in the inferior Waxwork II (Say what you will about Hickox, he
knows his continuity unlike some in the B-Movie world
)
I would think "Chop-Top" from Texas Chainsaw Massacre 2 counts even though he is family with his bosses. He is ceratainly the black sheep of the family after Drayton's (Relative) intelligence, Granpa's authority, and Leatherface's strength.
Fox, henchman to antihero-type Cholo from Land of the Dead simply disappears.
Does it count if a henchman outlives their boss by being their undoing? Dracula's Renfield lives, (in "Dead and Loving it"
) after accidentally disintigrating him, letting a beam of light shine through a hatch in the roof. Slightly similar example, 1964's Phantom of the Opera's dwarf assistant lives, though he accidentally kills his master anticlimactically. Something happened in The Rock where the mastermind was killed by his henchman,
because the mastermind was being too soft on his targets. Depending on your point of view, Gaear Grimsrud kills Carl Showalter in Fargo even though Grimsrud was apparently more experienced, Carl seemed (Comparatively) smarter and more devious, not to mention he acted like the one in control up until his death.