You can tell by looking at them, these are no ordinary Mooks. Every aspect of them is designed for maximum intimidation; their boots strike the ground with a despair-inducing tromp and their loud breathing sends chills up the enemy's spines. Their uniforms are black, possibly emblazoned with skulls, and almost always have a mask that makes them seem less human. Enemy soldiers would rather surrender than fight them, but they are trained to show no mercy. Every action they take is meant to induce Mook Horror Show in the Red Shirt Army and civilian populace.
In short, scary mooks, elite or otherwise. Expect a lot of Putting on the Reich.
Has nothing to do with the Web ComicTroops Of Doom, or the SNES game Doom Troopers.
Hellsing's Iscariot Organization soldiers wear armour and face-covering robes complete with conical hats of the kind traditionally worn during certain Catholic festivals — most commonly the burning of heretics by the Spanish Inquisition. This is clothing that citizens of the American Union have come to associate with the Ku Klux Klan.
ANBU in Naruto are supposed to be this. They are masked, nameless elites who carry out assassination missions and who hunt down rogue ninjas and dispose of their bodies to keep village secrets. The silliness of their masks and being the repeated victims of The Worf Effect somewhat ruins the effect, however. They're more of an example of Early-Installment Weirdness and don't really serve this trope after the arc that introduces them.
The riot police from Transmetropolitan have strong shades of this, what with having Submit Now emblazoned on their shields and taking Police Brutality to a whole new level.
Tiberium Wars presents the Black Hand as these; when a GDI infantry squad encounters a squad, the corporal in command completely flips out in terror at the sight. Later on, when a Black hand unit ambushes a GDI convoy, the mere sight of the Hands is enough to terrify a GDI officer into paralysis.
The 4Chan 40k parody army "Scary Marines".
While Imperial Stormtroopers from Star Wars are generally considered to be just Mooks, in-universe they`re greatly feared. In fact, the reason they're armored in white is to conjure up mental images of bleached bones. It's the black uniformed Imperial Army soldiers in bell-shaped open-face helmets that are the standard poor bloody infantry, and we see stormtroopers so much because we see Vader so much.
Their predecessors, the Separatist battle droids, were made in the likeness of alien skeletons. However, their stupidity and incompetence made them fail as Doom Troops utterly and completely (it didn't help that technical limitations resulted in the aliens in question being shaped differently enough from the droids that it wasn't obvious from the films that the droids were supposed to look like their skeletons). In The Clone Wars, the common "Roger-Roger" battle droids are, in fact, comic relief. Then they introduced the B2 super battle droids, which are much bulkier and more menacing than the B1's.
Warhammer 40,000 gives us two examples, the Death Corps of Krieg for The Empire and all the Space Marine chapters (both good and evil; it's explicitly stated that they eschew camouflage in favor of scariness).
Some sub-units take this even further: the Night Lords Legion of Space Marines have this as their hat, going into battle covered in the remains of their enemies, whilst the "Destroyer" units of regular Space Marine Legions were black armored chemical and biological weapon specialists. The reason their wore black? Because their weapons corroded the paint off their armor. Not nice.
In Strike Legion, not only do we have the Imperial Space Marines, who deck out their armor in Spikes of Villainy and bones and blood of their enemies, we also have the Doom Legion, made up of the most elite and well-armed soldiers in the Imperium.
The Coalition States of Rifts used to distribute suits of black body armor with an intimidating gas-mask stylized like a skull. Then they replaced those with suits of body armor sculpted to LOOK like a human skeleton.
Battalion Wars' Xylvanian Iron Legion. They even went so far as to make the already terrifying flamethrower emit a maddening, shrill wail.
Helghast from Kill Zone provide the image, although there's a large amount of evidence that points to them actually being the good guys.
Blackwatch soldiers from Prototype. Possible infectees are shown no mercy. In Prototype2 they're given a makeover to make them even scarier.
Star Wars Battlefront introduces the 501st, Palpatine's personal legion. In the movies you might remember them as the blue-striped troopers that Anakin led to the Jedi Temple. They also include the Dark Troopers, hulking cyborg troopers that were first introduced in Dark Forces. They wear armor similar to the Iconic Stormtrooper Armor, but painted black.
The Replica in FEAR. They're designed from the ground up to be implacable, fearless shock troops, and their armor makes them look greatly intimidating, especially when compared with ATC's baseline human soldiers.
Several examples in Fallout: New Vegas. The Legion Centurions who possibly are also Mook Lieutenant and the rarely seen Legion Vexillarii with their iconic armors. Then there is also the even scarier looking NCR Veteran Rangers with their ominous black armor and gas masks who send even the drugged fiends running for their lives, subverted that Veteran Rangers are the good guys and are some of the nicest NCR soldiers if you are in good terms with the NCR.
Proving that you can put Doom Troops in a game about gangsters, Ultor Corporation's Masako Team in Saints Row 2 is firmly in this territory. Sadly, Gameplay and Story Segregation is on full effect, as they are no more threatening (barring their larger HP) than your standard gangbanger.
NEO Umbrella's J'avo soldiers from Resident Evil 6 have all the standard Doom Troop gear, from full body suits to masks with ominous glowing eyes and puffy-face-organ-things. Thankfully they're only Doom Troops in appearance; in combat they're not any tougher than the other J'avo.
Guard regiments of XVIII Century and the Napoleonic era were often meant to look imposing, which was achieved by means such as enlistment of exceptionally tall men into their ranks, and uniforms including broad pauldrons and tall caps.
British Royal Marines
The Saddam era Republican Guard and Special Republican Guard.
The Italian Bersaglieri are a Subversion: they were intended as this and have the combat record and reputation to match, but their NiceHelmet◊ (created to help them aim their weapons, what with their name being Italian for sharpshooters) and propensity to run all the time, even when playing brass◊ (established by their regulations increase their stamina), make them look more ridiculous than scary until Fridge Horror sets in.