This was subverted very well in W.I.T.C.H.. The Big Bad's basic mooks are dumb orc-like guards who the heroines always beat easily. In one of the last episodes, they capture one of these guards alive, let him go... and he becomes a significant character in his own right.
Kim Possible has many examples of these. Lampshaded in "Odds Man In", when it is revealed that Dr. Drakken, in fact, did not pay his henchpeople but attempted to reward them with a large business-inspired incentive program (complete with trust exercises and org charts). Unfortunately for the villain, one of the good guys spread panic throughout the lair while incognito, convincing the henchmen to quit ("You know, 38% of all splinter mishaps are caused by manual lifting. Did you know you have a 17% chance of loosing your good looks practicing martial arts without the correct padding? Yep, one out of every two homemade explosive devices backfire.").
The codified hero/villain interaction in The Venture Bros. naturally involves henchmen; two, Number 21 and Number 24, become important recurring characters. Though they get beaten, maimed and killed on a regular basis, the henchmen frequently respect their enemies. (As one of them says of Brock Samson, "slayer of men, slayer of henchmen...".) Deconstructed a bit when it turns out that all of them except 21 and 24 have suicidal urges.
Various villains' henchmen make enough appearances that they could practically be considered a minor character, en masse. One episode even has a scene with The Monarch's Henchmen and Baron Ünderbheit's Henchmen sitting around a campfire discussing the reasons they went into henching.
The Monarch himself used to be a similarly number henchman for the Phantom Limb, Shadowman 9.
Æon Flux repeatedly and graphically deconstructs the mook trope. It's like the titular heroine is some sort of latex-clad ninja Hitler.
This is especially true in the Pilot and some of the early shorts. In the pilot Aeon comes in guns blazing left and right killing the faceless mooks, only for the heroism to be cruelly reversed when we see the survivors amongst mountains of corpses and ankle deep blood.
Perhaps a more notable deconstruction is seen in the short "War" which manages to blind the line between mooks and heroes by having a random mook kill the main character take off his helmet and become completely Bad Ass. He is then killed by another mook, in a double inversion of Why Don't You Just Shoot Him? and we follow his killers Bad Ass action sequence until he is shot by another mook, whose Bad Ass action sequence we follow through to the end.
Duke Igthorn's monster mooks in Disney's Gummi Bears. While technically being giant technicolor ogres, the dim-witted monsters rarely presented any serious threat whatsoever. Occasionally, the law of Conservation of Ninjutsu did apply.
The various flavours of Cobra from G.I. Joe fit the bill here. Mostly faceless (The majority wear full-face masks) disposable henchmen of various combat specialties in colourful uniforms - and they're all psychotically over-armed.
Sandman, Rhino, and Shocker tend to get this treatment in animated adaptations for Spider-Man even though they mostly work alone in the comics. Hammerhead even calls Marko and O'Hirn mooks in The Spectacular Spider Man.
The Transformers has Generic Gumby nameless Seekers in Season 1. In Season 3 they have the Sweeps.
In Transformers Prime, the Decepticons have the Vehicons (also known as Eradicons) who fill in the roles of standard mooks; they come in either car or jet forms.
Breakdown seemed to be on friendly terms with the Vehicons, acknowledging that guarding the Space Bridge was a thankless job.
The Insecticons have recently joined them. Conservation of Ninjutsu is in effect though; A single bug is still really hard to kill, but a swarm of them die in droves.
The Serpentmen in Conan the Adventurer, partly due to the heroes' starmetal weapons being able to easily banish them with even a single nondamaging hit.
The changeling army from My Little Pony: Friendship Is Magic's season 2 finale is a rare straight example of the trope from this show. Most other antagonists tend to avert it.
A weird subversion of this Trope appears in "Operation: T.H.E.S.H.O.G.U.N." The minions that the villainous Shogun Roquefort uses are actually competent and able fighters; however, Roquefort himself is anything but. When challenged by Numbuh Two, the villain is defeated when he hits his head on the ceiling and knocks himself out.