Something about a woman and an apple, I believe.

Joking aside, an answer to this question must come from an anthropologist / paleo-archaeologist rather than from a historian, since clothing by faaaar predates written history. To cite from the rules:

While there is a great deal of overlap, questions about early human history (beyond the written record), or proto-human history may be better suited to /r/AskAnthropology, and users should consider X-posting such questions there.

There's really no answer that is going to cover all societies at all times, so I'll focus on one particular time and place to give a single example which may elucidate general principles regarding taboos around nudity. That place and time is Mesoamerica around about the 11th-12th Centuries CE, and the particular people are the Mexica, who would become the core component of the Aztec Triple Alliance.

A defining moment in the Mexica origin, and indeed with all of the Nahua groups who trace their origin to Aztlan, is being summoned forth from the caves of Chicomoztoc by the Toltecs, who they saw as the originators of civilization. The Codex Tolteca-Chichimeca is perhaps the most famous depiction of nascent Aztecs emerging from caves to be greeted by the Toltecs. In the image linked above, the peoples leaving Chicomoztoc are shown on the bottom left, with the Toltecs facing them on the bottom right.

The imagery in this painting is complex, but the most important points to keep in mind for your question is how each party is dressed. The Chicomozteca are shown in coarse animal skin capes and simple breech-cloths, whereas the Toltecs wear full body suits reminiscent of the tlahuiztli overalls of elite Aztec warriors, made of cotton sewn all over with feathers. They are adorned with elaborate headdresses of resplendent feathers and one carries a long spear tipped with obsidian, as opposed to the bows and arrows of the Chicomozteca.

Encoded in this image are elements of the Mesoamerican distinction between "wild" and "civilized." The Chichimecs, clothed in skins and living subsistence lives hunting with bows and arrows, are contrasted with the Toltecs, who wear elaborate costumes, supported by a society of farmers, weavers, featherworkers, and others. Following Sahagún, the Aztecs recognized a gradation between the "teochichimeca" (true chichimecs) who lived entirely nomadic lives, the "tamime" who knew something of sedentary ways and might practice some horticulture, and the "otomi" who were an ethnic group in the northern part of the Basin of Mexico who were entirely sedentary but still seen as "barbarians" by the Nahuas.

A more dichotomous approach can be seen in Durán, who writes of the Chichimecs:

They were wild and rustic. And they were called thus because they lived among the peaks in the harshest places of the mountain, where they led a bestial existence, with no propriety or human organization. They hunted food like beasts of the same mountain and went naked without any covering on their private parts... The people slept in the hills, inside caves or under bushes, without any heed for sowing, cultivating, or gathering." (p. 16)

The description here matches Sahagún's "teochichimeca" who "had their homes nowhere" but "only went about traveling, wandering; they went about crossing the streams" (pp. 171-172).

The Chichimecs were, in Aztec thought, uncivilized nomads. Yet they were not necessarily looked down upon. They were seen as skilled in hunting, adroit with a bow and arrow, and knowledgeable of wild plants, both medicinal and psychotropic. They were noble savages, with an emphasis on the nobility, given that each of the three groups that made up the Aztec Triple Alliance derived their ancestry from the Chichimecs.

Yet, to become full fledged members of the urban culture of central Mesoamerica, these Chichimec-derived groups would need to undergo a process of civilization. For the Mexica, this was literally a divine initiation. Shortly after leaving Aztlan, the group that would become known as the Mexica were instructed by their patron god to seize a group of "mimixcoa," essentially a group of teochichimecs. Their god then instructed them to sacrifice these captives as tribute.

Once the sacrifice was complete, the group was given a name by their god, "Mexitin," which defined them as separate not only from the other groups migrating from Aztlan, but, more importantly, from the wild groups whose lands they were traversing. Attendant to this naming was the receipt of certain gifts, including feathered headdresses, bows and arrows, and a type of woven carrying bag. The Codex Boturini makes the transition to semi-civilized even more explicit by dropping the Aztlan name glyph at this point and literally showing an eagle dropping off these gifts to the group.

Along the way to what would become their home in Tenochtitlan, the Mexica picked up other trappings of civilization, including farming, the atlatl, calendrics, and cotton garments. They would also split with some of their companions, notably at Lake Patzcuaro. At that lake, a certain group petitioned their god to stay permanently, but the patron god of the Mexica had other plans. He instead counseled the main group to abscond with the clothes of the dissidents while they swam in the lake, leaving the unable to pursue the main body of the Mexica in their shameful nakedness.

Thus we have a perfect "just-so-story" illustrating the principal of structuralism, the anthropological theory associated with Claude Levi-Strauss. He hypothesized that cultures use dichotomous comparisons to define themselves and their society. These comparisons could include "cooked vs. raw" or "person vs. animal" and these oppositional categories could be used to delineate a society, the ultimate pairing being "us vs. them."

In Mesoamerica, the "clothed vs. unclothed" distinction was used to separate the "civilized" from the "uncivilized." On the one side were people who used the Mesoamerican calendar, grew maize, lived in houses, hunted with an atlatl, and wore clothes woven from maguey or cotton. On the other side were nomads who subsisted on wild game shot with arrows, and wore the rough skins of their prey. Clothes were a highly visible shorthand for a whole suite of other cultural practices which could mark an individual as either a member of the cultured in-group, or savage out-group.

Of course, all of this is relative. Even within Mesoamerican society there were distinctions between "high" and "low" dress, ranging from choice of fabrics to the use of sandals. The Spanish, upon their arrival, found Mesoamerican clothing practices among the stratified, complex, sedentary groups to be outside their norms for a cultured society. This just goes to show the constructed nature of human societies. Both elite Aztecs and itinerant Spanish, however, could both agree that clothing acted as a delineation between "civilized" and "barbarian." No discourse could even begin before that distinction was made, showing both parties they were operating on similar cultural plane. Even if their definitions of "clothed" differed, both groups knew intrinsically that they were not "unclothed."