The Order worships only Junil, but they are tolerant of the followers of Sirona and Lugus (but require the Priests of these other good gods to assist in their crusades, primarily as medics). (A lot of the Order's followers, especially among the Bannor, probably consider Sabathiel to be their god, but he is subservient to Junil. Also, the Temple of Temperance Civilopedia entry and the story of how The One created everything make me wonder if they also worship "Temperance," the orb that controls time, and the One himself. (Of course, the religion eventually became quite hostile to those serving the One, i.e., the Luonnatar.) I suspect that Junil may have originally intended the religion to be one serving The One and that he modeled it after the way thing were in the True Heaven, but then got caught up in the rituals and regulations and slowly fell away from his original purpose. That is a major problem with Law in general, and since FfH's gods are manifestations of their spheres they suffer from all the character flaws inherent in their spheres. I actually wouldn't be surprised if he were the next god to fall, although I don't think he would chose to join Agares so much as just become more harmful to his own side than helpful.)
The Empyrean is pretty clearly a Lugus worshiping religion. I suspect that they are even more tolerant of the worship of other good gods/goddesses than is the Order, especially of Sirona (We know that it values wisdom. Lugus is the god of Sun/light/Truth and Sirona of Spirit/Wisdom. These to tend to go hand in hand.)
The Runes of Kilmorph is pretty much just a Kilmorph only religion, as the name implies.
The Fellowship of the Leaves worships nature rather than a god, but in doing so they certainly venerate the gods most associated with nature: Cernunnos, Sucellus, Amathaon, and quite possibly also Arawn (they certainly seem to recognize the importance of death as a stage in the natural cycle of life. They likely also appreciate him gifting half of his domain to Sucellus). They probably also have some appreciation for Kilmorph (she is also the goddess of Autumn/Harvest), Danalin (plants need rain), Tali (also a god of spring, his storms help provide rain and spread seeds/pollen), and Lugus (at least if plants perform photosynthesis, which they probably don't) as well.
The Octopus Overlords religion does not worship a god; they worship dark entities created by the effective dreams of Hemah, who in turn was created by the the effective dreams of Danalin. These dreams are being horribly corrupted by the influence of Mammon's demons (especially Hastur), but they aren't in control of them. Elements of good may still remain in Danalin's, and thus Hemah's, dreams, so the Overlords aren't entirely evil. They are certainly not the same beings as the demons that are twisting Danalins dreams, and these demons aren't worshiped by the OO. (On the other hand, it was based on numerous cults that worshiped various Beasts, most of which were Demons of Mammon who had gotten lost in Oghama's mists and forgotten who they were. But the Octopus Overlords never really existed in Kaels campaigns, so I prefer my fist explanation.)
The Council of Esus naturally venerates Esus, however, the nature of the religion makes me think its followers probably aren't very devout followers of any of the gods. (Of course, they would be willing to feign devotion to anyone, but only for selfish reasons of their own.)
The Ashen Veil serves the many denizens of Agares's hell. Foremost among them Agares and Bhall, but they'll really serve any of the evil gods that give them power. However, I would say that the religion is actually mostly Autotheistic; its followers do whatever they can to gain god-like powers for themselves, despite hating and fearing those they serve. I'm not sure whether I would call what they do worship either.