Now Mystara didn't have gods, but Greyhawk does and so do all the other worlds I am using here.
A few I know I am going to use and where they all fit.
Gods
Ancient beings of great power. The next generation after the Titans and Primordials. Gods differ from humans and the others in many respects. Gods can have Aspects and Avatars, which are semi-independent versions of themselves that can interact in the world. Demons and Devils can have Aspects too, but generally only one at a time and for them it is more like Astral Projection.
Gods also have the power of creation. They created their specific races, or the lands, or even the world.
Bahmut and Tiamat -Bahmut (and his Dragonlance cousin Paladine) has become the god of Lawful Good paladins since the 3.0 days. This is only reinforced in 4.0. Plus he is a very D&;D god, with ties back to the first Monster Manual and featured in the Dragonlance sagas.
Tiamat is a given for the same reasons, but she was also a god in myth in her own right. Though given that in Babylonian myth she was the god of Chaos, I would change her alignment from LE to CE and put her in the Abyss. In fact the Abyss is there there because she was tossed into it.
Sehanine / Selûne / Shar - Three aspects of the same moon goddess. Represent the Maiden, Mother and Crone aspects of the Triple Goddess. Neutral.
Wee Jas - Goddess of Magic and Death. The Witch Queen. Worshiped by the Suel. Mix in bits of Hecate, Cardea, Isis and Mystra to her. Her student was Ioun. LN.
Others
Bast Egyptian - Goddess of Cats and the hunt. CG
Blibdoolpoolp (Greyhawk) - Goddess of the Kuo-toa and other deep see nasties. Maybe a daughter of Dagon and consort of Demogorgon (ick). CE
Camazotz (Aztec) - the Bat God, I like having him as the god Vampires too, great rivalry exists between him and Orcus. Camazorz doesn't control vampires, but some vampires and vampire cult pay him homage. CE
Celestian (Greyhawk)- God of the stars. Have to include him. Neutral
Corellon - God of Elves.
Gruumsh - God of Orcs. Neutral Evil.
Istus (Greyhawk) - Goddess of Fate. Neutral
Lovitar (Realms/Finnish) - Everyone needs a crazy S&M chick.
Set - God of Evil.
Surtur - Fire Giants and Thrym - Frost Giants, both from Norse myth, but folded into the D&D myths.
Vaprak, the Destroyer - God of Trolls and Ogres. Though I have considered having this just be an aspect of Demogorgon.
I plan to use Earth myths when I can. For example my Desert Elves worship elven versions of the Egyptian Pantheon. Isis is an elf, but Set is human since according to these elves humans are the greatest evils in the world.
Devils
The new editions of D&D (3.x, Pathfinder and 4) have Asmodeus listed as a god. Now I have no issues with that per se. I even think the back story of Asmodeus rising to power that started with the Dragon Mag article "Politics of Hell", on through the Blood War stuff and finally his triumph at becoming a Dark God is an interesting one. But it does't work for me. See I would rather set Devils up as the alternatives to Gods. The devils temp mortals away from the "proper" religions to worship them. Why would a mortal worship a lesser beign like a Devil? Simple, the devils provide a quick avenue to power. Gods, even evil ones, require faith and worship and service, the rewards then are given based on that faith. Devils tell the mortals "hey, why do all that work when you can work with us and get all those benefits now." Devils also side with mortals against the Gods. They will remind mortals that the Gods have it easy while they work and toil. They even try to promote kinship, "hey the Gods cast us out, so we are on your side." Of course these are all lies, but situated in enough truth that mortals keep falling for them. Asmodeus then is not a Dark God, but the most power Arch Duke there is and his power is equal to that of a god or goddess. The Devils will even point out that one of their own rose to such power that is should be possible for everyone to do it.
The devils now have moved beyond the "Blood War" of 2nd ed and are now going to engage in a "Gods War" with the battlefield the mortal realms. I think a good story for the PCs would be to become part of this "Gods War". I alluded to it a little in my Buffy adventure, The Dragon and the Phoenix.
Afterall what would be more climatic than all the heroes, each representing their God, on the field of battle against the greatest foe in humanity. I might drop my "Vs. Orcus" idea for this instead.
Demons
The Abyss is the sewer of the multi-cosm. Everything that gets flushed, thrown out, discarded and forgotten ends up here. Of courses there were plenty of things here to start with. Demons are legion. There are thousands of types, races, and varieties. Some, like Orcus, are "dead" Gods. Others, like Demogorogn, used to be Titans. Others still are cast out gods (not sent to Hell), forgotten powers or even monsters that have become very, very powerful. There are even ones that were spawned by the Abyss itself. If the ultimate purpose of the Devils is the destruction of all the Gods, then for Demons it is just destruction.
The Blood War, the war between the Demons and the Devils, was a minor skirmish in the long range plans of the Devils. In fact prior to the Blood Wars, demons and devils had been on working terms. The devils would often use demons as grunts in their battles. This went on for so long that some species of demon were once considered to be devils and visa-versa. Graz'zt, the Demon lord, had been an Duke of Hell, till he went native. Succubi are constantly switching allegiances between demons and devils that they are difficult to properly classify.
Demogorgon - Older than the gods. A Titan that has become more demonlike. Hates Orcus. Only worshiped by non-humans and insane cultists. Just wants to destroy everything. CE.
Jubilex - Demon lord of slimes. Created from the Abyss itself. It is as if all the waste and runoff of the Abyss collected into a conscious form. Deeply, deeply insane. Wants the entire multcosm covered in acidic slime.
Orcus - Was a god, then demonized, killed, came back as undead, became a demon again. GEnerally just an angry dude. Hates undead, but hates them less than he hates everything else. Wants to become the God of the Dead. CE.
Primordials and Titans
Like in Greek myths, the Titans were the "parents" of the Gods. Some gods from other games might end up here. I prefer to figure these out as I need them. The Scarred Lands books from Sword and Sorcery Studios were good for this concept as well. They had a lot of interesting titans. Theirs though were outright evil, I prefer to have my titans more uncaring about humans. The world was theirs, now it isn't anymore and they are not happy about it. Most of the titans are dead, others are imprisoned or converted to demons.
Primordials came even before the Titans and represent raw nature or natural aspects of the world. Earth, Sky, Night, Death. These things are hard to personify into human terms so Primordials are not really like the gods or titans at all. Primordials do not care about worship or humans although some are aware of such actions. In some cases my "Titans" are what other games "Primordials" are and my Primordials are something different.
Mad Gods
Have to include these. Things like Leviathan, Cthulhu and the rest certainly will have a place in my game.
For me Gods need to be complicated. The characters live in a world where they can travel to the planes, commune or other wise get "evidence" for their faith. I think I might make this a bit tougher is some cases and even out right prohibit in others.