As above, Terry Pratchett not only subverts, but smashes, immolates, and urinates on this trope with Guards! Guards!! and, indeed, any book that stars the Ankh Morpork City Watch. People who have read these novels often have a hard time, thereafter, accepting city guards as nothing more than a mild threat to the hero. Even Nobby and Fred, ineffective coppers in every sense of the word, manage to be more competent officers than your standard fantasy watchman. The whole matter could be because standard fantasy officers are nameless, sometimes faceless, and effectively rankless since they're going to die anyway, while the average Ankh Morpork copper usually even has a personality, much to the envy of his friends on other worlds.
This may be due primarily to Pratchett's compulsive character-deepening. Originally, Guards! Guards!! was going to be about Carrot and told from Carrot's perspective, but Pratchett found that Vimes had way more character to him than he expected, so he wrote it from Vimes' point of view. Every character he introduces into the watch ends up with a rather definable personality, even those who seem like cheap jokes based on The War on Straw. Constable Visit-The-Unbeliever-With-Explanatory-Pamphlets ends up with a fairly rounded personality even by the end of his introduction.
Guards! Guards!! also has a side-example in the genuine Mooks of the Palace Guard, who are Genre Savvy enough to be terrified at the prospect of facing a single, unarmed, smiling foe: after all, that is statistically the most dangerous kind of enemy.
In The Last Hero, the Genre Savvy Silver Horde realized with horror that when Carrot showed up on the scene, alone, to arrest them, they themselves had become the mooks.
In Small Gods, Urn, a junior philosopher, speculates that it'd make things easier to think of people as "gooks" during warfare.
Mercenary Song, a poem by Hungarian author Gyorgy Faludi, tells the everyday lives of mooks from their perspective. It involves the titular mercenaries proudly bragging about every single atrocity they committed, including breaking into people's houses, eating all their food, raping their wives, selling their daughter, and clubbing them to death if they don't say 'thank you', killing their own parents, cutting down all the trees, poisoning all the wells, just because they enjoy it, and specifically stating that they serve whoever pays them the most, quite possibly making them even more evil than their employer. The poem ends with them growing old and senile, living as beggars for the rest of their lives, barely surviving and only thanks to the mercy and goodwill of the very same people they loved to abuse so much.
The Draka's janissary troops are treated like expendable Cannon Fodder in military situations ranging from direct frontal assault to anti-partisan duty, as that is their purpose within the Domination's military hierarchy. The Draka's enemies usually only view the death of Citizens as meaningful.
The Godswords are this in the first Shadowleague book, before their collective Heel-Face Turn. It makes one wonder why more mooks don't switch sides.
In the Harry Potter series, a handful of Voldemort's Death Eaters are significant villains in their own right, but most are mooks with names, albeit usually just a sinister-sounding last name with no mentioned first name. In the movie version of Deathly Hallows, actor Peter Mullan took Yaxley, one of the background generic Death Eaters in the books, and gave him a bit of character, playing him as sort of a classy gangster type.
Most of the Malwan army in Belisarius Series. After reading awhile you wonder just how this army is supposed to Take Over the World or even threaten to take over India. Especially when you consider that the Roman army is on the other side.
In The Wonderful Wizard of Oz, the Wicked Witch of the West had three armies of Mooks that she sent out to deal with the heroes when she first realized they were in her domain, and the heroes dealt with them rather easily. The first was a pack of savage wolves, which the Tin Woodsman was able to slay with his axe. The second was a flock of attack crows; the Scarecrow was able to lure them to him, then grab each and break their necks. (Maybe he was better at his job than he initially had thought.) The third group was a swarm of killer bees which the heroes defeated with a rather clever idea: The Tin Woodsman took the Scarecrow's straw, and used it to cover Dorothy and the Lion, hiding them, and when the swarm descended, the Woodsman was the only one they saw. But when they attacked him, they broke their stingers against his metal body and were killed. After this, the Witch sent her Winkie slaves to deal with them, who may have counted as a fourth group, but they really weren't fighters; the Lion simply scared them away with a loud roar. This forced the Witch to use the third - and last - use of a magical hat that let her command the Winged Monkeys, who might count as Elite Mooks; they did not fail, but fortunately, the heroes survived and eventually escaped.
In Frostbite, Isaiah the Strigoi employed human Mooks to capture his Moroi and dhampir enemies, and keep watch over them. They mostly used guns and regular equipment to keep control of their captives.