At various points he's also been seen in a tank top, especially during his stint as a wrestler. The amount of clothing he's wearing at any given time probably has to do with the artist's deadlines as much as anything else.
The Mole Man from the Fantastic Four series has an army of Moloids and monsters of varying intellect. More often than not, they all wear multicolored underwear and little else. Odd considering that Mole Man is fully-clothed, highly intelligent, and wants to turn the Moloids into a proper civilization.
The Beast from X-Men is another fine example. He started off looking reasonably normal. During this time, he was covered up almost completely. Once he turned into a furry monster, he stripped down to underwear. This is especially odd since the character is a very educated, polite individual who would normally be the type to dress in a dignified manner.
Hank explained at least once, though it may not have been fully serious (or even canonical), that he dresses the way he does because all that fur got downright HOT when all covered up. When he DOES get fully dressed, he's about as dapper as a bulky, stocky man with bright blue fur all over his body can be.
Averted/Justified in the movie, where he is in a suit half the time, fitting his status as a high-ranking politician, and when he gets into his X-uniform, his open jacket is justified with something along the lines of "I can't believe this used to fit me".
Another interesting case from the X-Men is Colossus. He is normal looking but can turn himself into a metal humanoid. Usually, he wears very little, showing off his metallic form. In his earlier appearances, Marvel Comics editors felt it was unacceptable to have a half-naked man but it was fine if he was made of metal at the time. Because of this, Colossus was shown in full-glory while in his metal form but when it came time to change back into a human, the bare parts of his costume were colored blue. This mandate didn't last long, though.
Justified in that, who wouldn't want to show off if they were that ripped? In fact, as recently as Joss Whedon's run when his powers are off his costume has become as Female Gaze friendly as it should logically be.
To be specific, it's the savage green Hulk who usually just wears pants. When Hulk gets a bump in intelligence he often starts wearing clothes. For example, when grey Hulk was thought to be dead and was free from transforming back into Bruce he lived a more normal life and developed a taste for tailored suits.
She-Hulk likewise wears very revealing clothes with a combination of this trope and Fanservice.
During Marvel Comics' monster-era, many of the monsters would wear a pair of underpants. They ranged from giant space dragons such as Fin Fang Foom to radioactive creations. The non-sentient monsters didn't make much sense, considering they shouldn't know enough to have any modesty while the intelligent monsters should be a bit more selective in what they wear. Case in point, the aforementioned Fin Fang Foom, a giant alien dragon that is from such an advanced race that... they are apparently okay with walking around in underwear.
The animated and live action versions of him gave him long pants, boots (the comic version had hooves), and sometimes even a shirt.
Spoofed in B.P.R.D.: When he was introduced, Ben Daimio insisted on having Roger wearing pants. But after actually seeing (a very proud) Roger wearing them, Ben told him to take the pants off again because he looked ridiculous.
The Absorbing Man from Thor can morph his body into anything he touches (if he touches steel, then his body turns to steel). For whatever reason, he often goes shirtless.
Pip the Troll from Marvel Comics' Infinity Watch usually just wore a loincloth: attire usually suited for savages.
In fact, many characters on that team had pretty Stripperiffic costumes. They were all aliens, genetic creations, or otherwise metahuman. The guy in the background of this◊ picture wore a cape but also ran around in underwear at different points in his career.
Mephisto, also from Marvel Comics, is an odd Eldritch Abomination example of this trope. He's the MU's version of Satan but he often wears a loincloth and cape with nothing else.
Martian Manhunter wears a cape, underwear, and a weird x-shape vest that barely covers his chest. Not only is he highly intelligent, he is also a Shape Shifter so he could very easily form a nice suit if he wanted to.
On the other hand, maybe the shape-shifting just makes the Martians indifferent to anything related to physical appearance, clothes/nudity included?
Or he wears the uniform of a Manhunter (police officer) as seen in the 1998 Martian Manhunter series
For Dr. Manhattan of Watchmen, the level of clothing he wears at a given point of time indicates his growing detachment from humanity. At first, he continues to appear fully dressed after his transformation. But as time goes on, he pares down the uniform more and more until it's barely there at all (just speedos, then literally nothing). (His last TV appearance creates a capsule version of this, going from a rather smart suit on the set to pretty much nothing after his abrupt departure cuts his last ties to Earth.)
Wildguard featured the massive rock-man Crag Langley among the contestants vying for a spot on the titular team. Crag doesn't wear a shirt because the large. craggy protrusions on his back would make doing so look really stupid. He does, however, wear pants and boots.
Inverted in Atomic Robo: the titular Ridiculously Human Robot always wears full pants and usually wears a shirt and sometimes a hat because it helps him fit in better (or as he puts it "I wear pants because it's the law").
Tigra is a Cat Girl who usually walks around in just a bikini. Like in the Beast example above, it's been explained that having fur all over your body makes any other style of clothing both impractical and overbearingly hot - and since she's now operating out of Los Angeles, it'd just make things worse.
Films — Animated
The Beast in Beauty and the Beast wears only pants and a cape. As the story progresses he wears more clothes and Word of God said that if Belle had never showed up eventually he would have stopped wearing clothes entirely.
Films — Live-Action
Sean and Patrick in The Monster Squad engaged in some Conversational Troping about this trope in regards to the Wolfman in an earlier scene. Sean points out that the Wolfman had to wear pants because those movies were made in the 40s and they didn't want us to see his..."wolf dork." Yeah.
Discworldtrolls (except Detritus, who wears a Watch uniform, and Chrysophrase, who wears a suit) mostly just wear a loincloth "to conceal whatever it was that trolls found it necessary to conceal."
Golems usually avert this (some have been painted to resemble clothes, but in any case they lack attributes), but Going Postal has Gladys the Post Office golem, who wears a dress ( and is called Gladys) because Miss Maccalariat objected to a "male" golem cleaning the ladies' restrooms.
Discussed in The Bartimaeus Trilogy. Bartimaeus appears to Kitty in a monstrous, demonic form in order to intimidate her . . . and Kitty tells him to put some pants on. Bartimaeus is baffled by this, as he's never bothered with clothes in that form and didn't think they would go with it very well. Kitty recommends Lederhosen.
Then again, when he's in human form he apparently just wears a loincloth if he can get away with it, so maybe spirits just have different standards in general.
In Rainbow Magic, the goblins wear loincloths when not disguised, and full human outfits when in disguise. In the movie, they also wear shirts and pants.
In World of Warcraft, a number of mobs are bare skeletons that still inexplicably wear something like shorts or a short skirt around their hips.
Goro and Kintaro from Mortal Kombat both wear black briefs, though there have been more substantial variations on their costumes over the years.
This was blue for Goro and red for Kintaro, at least in the comics and novelizations, but obviously black in the video games. After adding a loincloth to Kintaro's design (he's still wearing the black briefs beneath it) in Mortal Kombat: Armageddon, they seem to have followed this pattern with Goro in MK 9, adding a loincloth and various accessories (wristbands, etc) to Goro's outfit.
Not to mention Sheeva, who's a female Shokan, who wears a Stripperific outfit. This is the source of more attention from fans than a four-armed muscular brawler would suggest.
The later Geneforge games lampshade this—thahds don't care whether or not they're clothed, and the Shapers that made them are too familiar with thahd anatomy to be concerned about the subject, but thahds that are around outsiders must wear loincloths to avoid "offending delicate sensibilities."
Blanka from the Street Fighter series wears torn brown trousers, showing off his bulky, green, orange-haired physique.
The Seeq from the Ivalice Alliance often wear just loincloths instead of pants and when they wear shirts they cover very little. Somewhat odd when compared to other races such as the Moogle, Bangaa, Garif, and Nu Mou who are fully or mostly clothed. It is justified for the Seeq since they are basically a race of obese pig men, thus most clothing would not fit them.
The Gargoyle race from the Monolith FPS Blood wear absolutely nothing, accessories or otherwise. While you always encounter them simply as enemies to deal with, the story information and character bios seem to indicate that they are sentient and do possess intelligence to interact on-par with humans. Nevertheless, they are always seen completely in the flesh (literally, as the common variety's full name is "Flesh Gargoyle"). This coupled with their skinny body physique tends to make their choice of attire stand out as well.
Dark Souls has the Capra Demon. A demon that resembles human with a skull for a face. It inexplicably wears pants. In the Updated Re-release, there are plant monsters that also wear pants for some reason.
Dimetrodon is a superhero/ humanoid dinosaur wear nothing but short pants in Legacy Of Heroes.
The Bokoblins in The Legend of Zelda: Skyward Sword either wear clothes or go without, but they always have some form of underwear worn, to which your companion comments about when you ask her for enemy info. There's also a Running Gag of all the Bokoblin species being obsessed with their undergarments.
In Goblins, some of the characters, particularly the monsters released from the dungeon in Brassmoon City fit this trope
The Gargoyles are certainly intelligent, but apparently don't feel the need to wear anything more than loincloths.
It's specifically mentioned that Gargoyles don't share all their values with humans, and heavily implied that they cover up as much as they do so as not to creep their human friends out. At least, the ones from 10th century Scotland are like that, gargoyle tribes from other areas (and times) have varying levels of dress.
Interestingly, the main cast's elderly member is significantly more dressed than the others. Out of universe, a potbellied, beige-skinned old man would look stranger in a loincloth than the others. In-universe, he could use an extra layer of leather for protection since he's not as agile as he used to be.
Omniverse plays with this with Rath, a tiger man alien form who is never clothed. When Ben meets other members of Rath's species, he's rather shocked to find out they normally do wear clothes, meaning any time he fought as Rath he really was, by their standards, running around bare-ass naked.
Averted with the initial design of The Annoying Thing, also known as Crazy Frog. It appeared in ads and music videos sporting ambiguous genitalia which, after complaint, were eventually censored (with pixelation or black bars) in many locales and later removed from the design completely.
Averted with real world monstrous animals (bears, rhinos, sharks, etc.). While they're not wearing shorts, most predators do not have noticeable genitalia, so there's no real need for modesty. It's either retracted, covered in fur, or small enough to be ignored. People forget that humans have a dis-proportionally large penis as compared to other predators. So when artists and authors started making humanoid monsters, old timey morality standards required them to draw them covered up.