Let’s dispense with the obvious: if you just want a bunch of crazy people in robes screaming about Hy’Fhen-Ator the Gore-Drenched while your player-characters (PCs) are busy burning down the Hy’Fhen-Ator’s Dark Temple, you don’t really need advice. Evil crazy cultists with a barking mad deity and an uncritical willingness to throw stupidly dangerous spells around: yes, that will be fine for many an adventure. And I don’t mean that sarcastically, either. Sometimes the PCs (particularly, the paladin-types) just need to really cut loose and Smite some Evil, right? After all, that’s why the players wrote them up in the first place.
But if you’re looking for something a little different, that’s fine, too.
We’ll assume, going in, that your cult is in fact evil. If it’s not evil then it’s probably at worst a weird, persecuted religious minority and those are not really fun to Smite anyway. But is the cult EVIL? Does it have a direct link to Something Bad?—That’s not the same as asking if it has access to magic, necessarily. In some game worlds baker’s guilds have access to magic. But is the cult actively making deals with demons, using the life force of babies to fuel its spells, or deliberately trying to destroy the world? Or are they ‘just’ doing the more mundane sorts of evils, like human trafficking, sedition, or building a criminal empire? This can be important if the PCs think that they need to bring enough firepower and urge for destruction to handle the first category, when in reality the cultists are in the second category—and are thus more likely to simply sublime in the blast wave. If nothing else, the local government might thus be inclined to object more if the destruction is too comprehensive.
But even if the cult is EVIL… why? What is the motivating factor for a cultist to sign up for eventual destruction? It’s easy enough to assume that cultists are primarily the weak-willed or the already-evil, but the first type does not make for particularly difficult opponents and the second does not make for particularly interesting ones. Of course, this problem has been considered, before: which is why ‘revenge for transgressions done unto me’ is also a popular justification for joining a nihilist death cult. And that’s fine, as long as the gamemaster (GM) puts some effort into coming up with a really good backstory for it. In fact, I would suggest that GMs interested in doing this take the time to track down David Drake’s excellent “Than Curse The Darkness” (found in his short story collection Balefires). In that story Drake justifies the existence of an entire, ‘classic’ Cthulhu Mythos cult—gleefully self-destructive and all—with a simple “They’re living in Emperor Leopold’s Congo Free State.” Which is both defensible, and a good example of what level of horribleness would probably need to take place to make Dark Gods look like a not completely unreasonable alternative.
And then there’s the pragmatic aspect of it all. What is Cult Life like? Do they live in monasteries? Then what do they eat? Who grows the food for them? Who cleans up after them? Why haven’t the locals burned out the place (even cultists have to sleep sometime) yet? Or, if they’re in an urban setting… having a sewer lair is all very well, but what of the smell, not to mention the various disease farms down there? Or does the cult just have an upper room for meetings and sacrificial offerings somewhere downtown? If they do, what do their neighbors think? What’s their favorite restaurant or tavern?—And, yes, that’s a fair question for non-monastic cultists, even evil ones. If they’re in the world, they’re going to be of the world; and if they’re small-e evil and generally pleasant enough to people who are pleasant to them, they might even be able to count on the other patrons in their favorite watering hole to take their side when the PCs rush in and start a bar brawl. That should give your characters a moment of befuddlement, especially if said bar patrons are obviously not actually evil.
Again, there’s nothing wrong with giving your PCs a Dark Cult or two to Smite. But if you’re looking for something more elaborate than that, it’s certainly possible to come up with something else than a simple ethical reversal that makes the Dark Cult actually a bunch of brooding, fundamentally nice people who quietly grab orphans off the streets in order groom them into becoming unstoppable agents of mercy and grace. …Although, honestly, that’s kind of interesting, too.