For the purposes of this article, I am going to stick (mostly) to the so-called "Gold Box" release of The World of Greyhawk. In part, this is because I like 576 CY campaigns and the freedom they give for the individual DM to develop the setting as they see fit. I also take the events in the Greyhawk's World series of articles found in Dragon magazine from 1981-1982—and to a lesser extent the Deities & Demigods of the World of Greyhawk series of articles (and Gods of the Suel) that appeared in that magazine from 1982-1984—as mostly canonical, though I reserve the right to change anything in those articles to suit my purposes. So, I suppose you can call it a 578 or 579 CY campaign. One of the more obvious elisions in this article, then, will be the Elder Elemental God, Zuggtmoy, Lolth, and so on, except of course for Iuz. I'm also going to skip over the demihuman and humanoid pantheons as they are mostly disconnected from the main subject of this article.
Pretty obviously, the list of gods in the Guide divides the gods into four main "ethnic" pantheons (though, as we will see, things are not so cut-and-dried): the Oeridian, the Suel, the Flan, and the Baklunish. A number of the gods from each of these pantheons are also included in what is termed the "Common" pantheon, which we can imagine is the pantheon of gods imagined by people who aren't particularly connected to any of the particular religious expressions in the Flanaess—the gods of the common people, if you will. This Common pantheon includes all of the gods of the Flan, most of the gods of the Oeridians, a very few of the gods (to be exact, two goddesses) of the Suel, and the lesser gods of the Baklunish. In addition, the Common pantheon includes a number of gods unconnected to the other pantheons, and for the most part not to each other except for their inclusion in the Common pantheon.
It is important to note that Gygax noted that the "Greater" gods see very little actual worship, being too big to be credible in responding to the needs of some shepherd in the Hestmark Highlands or whatever, so most of the religious activity of those who are not actual clerics or the great nobility is concentrated on the so-called "Lesser" gods and the demigods.
The Flan pantheon consists of nine gods, four "Greater" gods, four "Lesser" gods, and the Demigod Iuz. The four Greater gods are Beory, the Oerth Mother, Pelor, the god of the Sun, Nerull "the Reaper", god of Death and the Underworld, and Rao, god of Reason and Serenity. This is mostly the typical "pagan" pantheon envisioned by neopagans in the real world today with the addition of a god of Reason. We can perhaps envision a central myth similar to the "Oak King-Holly King" one that developed among neopagans in the 20th century, where a great Goddess is alternately wed to a God of summer and a God of winter, changing at the equinoxes or solstices (or perhaps at the midway point between an equinox and solstice) when each God meets the other in combat and the winner takes the bride. That is, a typical seasonal myth. It's up to the DM how they might want to envision this myth as a rite, perhaps varying from place to place in the Flanaess.
The "Lesser" gods of the Flan include two who are connected to the world and two who are associated with social behavior. The two worldly gods are Berei, goddess of the home and agriculture, and Obad-hai "the Shalm", god of nature and the wilderness. The social gods are Allitur, god of ethics and proper behavior, and Zodal, the god of mercy and hope. Iuz, of course, is a demigod whose machinations drive the overarching action hinted at in the existence of the land named for him as well as the opening moves described in the Greyhawk's World articles and of course the events in such classic adventures as The Village of Hommlet.
The Oeridian pantheon is much larger, but has only two "Greater" gods, Procan, the god of oceans, and Zilchus, the god of power, prestige, and money. I envision the former as the god of the physical world, which the Oeridians must understand as arising from the surrounding ocean, while the latter is the god of actions, understood as the powers of the nobility to command, the "invisible hand" of the market, and so on.
Similarly, the "Lesser" gods of the Oeridians can be divided into gods of the physical world and gods of mental states that drive actions. In the former case we have the gods of the four winds and their associated seasons, Atroa, goddess of the east wind and spring, Sotillion, goddess of the south wind and summer, Wenta, goddess of the west wind, autumn, and the harvest, and Telchur, god of the cold north wind and winter. In addition, there are Celestian, god of the stars and wanderers, Fharlanghn, god of the horizon and travel, and Velnius, god of the sky and weather. Pholtus "of the Blinding Light" stands, perhaps, in between the physical world gods and the mental gods, being god of light but also of law. To a certain extent, Pholtus seems to have developed as a nearly monotheistic god, jealous of other deities, at least in the early material about him.
The rest of the Oeridian gods include Delleb, god of reason and intellect, Erythnul, god of hate and envy, the very similar Kurell, god of jealousy and revenge, and the opposing pair of Heironeous, god of chivalry, honor, justice, and valor, and Hextor, god of war, discord, and massacres. Finally, there is the demigoddess Rudd, associated with both chance and skill. Of these gods, only Delleb, Velnius, and Kurell do not make the leap into the Common pantheon, perhaps because Kurell is difficult to differentiate from Erythnul, Velnius seemingly duplicates the four wind gods, Pholtus, and Celestian, and Delleb is maybe seen as a lesser version of Rao.
The Suel pantheon is commanded by three "Greater" gods, Kord, god of athletics, sports, and brawling, Wee Jas, goddess of magic and death, and Lendor, god of tedium and the passing of time. This suggests a culture that values on the one hand physical activity and on the other the uncanny, but considers all other events to be merely wasting time.
The "Lesser" gods of the Suloise include an interesting mix that deserve some contemplation. There are four goddesses, Bralm, goddess of insects and industriousness, Lydia, goddess of music, knowledge, and daylight, Beltar, goddess of caves and malice, and Syrul, goddess of deceit and lies. In addition, there are seven "Lesser" gods, Fortubo, god of metals, stone, and mountains, Llerg, god of beasts and strength, Norebo, god of gambling and luck, Phaulkon, god of wind and clouds, Phyton, god of beauty and nature, Xerbo, god of the sea and money, and Pyremius, god of fire, poison, and murder. Of all of these gods, "Greater" and "Lesser", only the goddesses Bralm and Lydia are to be found in the Common pantheon.
The Baklunish people hold Istus, Lady of Fate, to be the greatest, and under her are two "Lesser" goddesses, each pointing the way to a different way to meet fate. On the one hand is Xan Yae, goddess of stealth and shadows, but also mastery of mind over matter, and on the other is Geshtai, goddess of rivers, lakes, and wells. The one demigod of the Baklunish people mentioned is Zuoken, associated with physical and mental mastery, who maybe can be understood as the consort or son of Xan Yae, or perhaps her devoted follower. Of these, only Istus is not widely worshiped in the Common pantheon. My own take on this pantheon is to draw parallels to medieval Islam, with its focus on fate being previously written, and the "Lesser" goddesses being representative of an appreciative and aesthetic approach to meeting fate, and an approach to fate of mastery, suggesting a Sufi-like mysticism or, alternately, cults of assassins exerting their will.
Anyway, this has gotten long, so I'll save the rest of the gods, unassociated with any particular pantheon, for another time if there's any interest. That's where you'll find St. Cuthbert "of the Cudgel", Boccob "the Uncaring", and the nearly-Lovecraftian Tharizdun, among quite a few others.