I have a home setting called Cantadel for most of my D&D 3.5 and 5e games. It's a pretty generic setting, I think, but I think a few specific pointers can be brought out...

For starters, a couple villains...
-Thuzdek the Undying: a kind of psychic mummy who was able to create bifurcations of himself, so that there would always be more of him around if his corporeal vessel died. So, you have many thousand beings who all claim to be Thuzdek, and all of them are correct. While they all agree that the "original" Thuzdek is the leader, they generally live their own existences, being Thuzdek in their own way elsewhere (many aren't even human or undead. Thuzdek is also a number of powerful young dragons, a merman, a sentient lion, and many unspeakable things that should not be among others.) Whichever Thuzdek you deal with, know that Thuzdek controls an entire continent, and a great amount of territory on other continents. He was a deplorable villain despised by all who knew his name when he first conquered those territories, but over the past few thousand years people have just grown to accept that he's the one in charge of those places. He's still villainous and a schemer, but he's also an institution at this point.
-Braxton Barnes is a low-grade magician who's never really been taken seriously but has the potential to be a big problem. He's a little too wiry to truly rock the traditional wizard robe and pointy hat (he prefers greens and blues), but he's noticed by many thanks to his koala familiar, that mostly keeps to itself on his hat. Braxton is usually a lackey of wealthy thieves guilds or powerful nobles or others who are acting as the "real" villains, but he's made a name for himself among humanoids; your average person in the street hasn't heard of him, but the people they *have* heard of usually have. The same can't be said for his familiar, though: the koala doesn't move much, but has a strange aptitude for organizing other koalas and their kin (including the monstrous Drop Bears) into surprisingly capable ambushes. Other koalas and drop bears know the familiar, though they don't talk much (and are fortunately limited to certain places in the world.)
-Xol, queen of flame and fey, is the inventor of "The Flame that Burns Lives". Certain sinister fairies and fire creatures obey her as if it's a natural part of existence, much as a human might obey "the need to breathe". She doesn't need to order a red dragon to destroy that village, she just entertains the notion long enough for the red dragon to do so. It was the red dragon's idea, after all.
-The Falcon Queen is the leader of a surprisingly non-magical nation, and is highly paranoid about the magic rich nations that exist nearby. Named for her love of hunting and falconry (and certainly aided by her skill with a bow, unparalleled even by those divine beings who have tested her), she's made certain deals with elemental figures from other realities, such as the genie Lord Fulgurite, who believes that her paranoia will lead to international incidents that will fuel the chaos that makes his chosen element, Storm, more powerful.



Then there's magic...
-I have a semi-built NPC class called The Magician who acts as a sort of arcane (more on that later) counterpart to The Adept (though sometimes Eberron's Magewright class can fill in the gap depending on if I'm going for a "Let's call the magic handyman" approach instead of a "Let's consult the hermit who lives on the mountain" kind of thing.) This handles everyone from the "mighty wizard" who's little more than a commoner who can cast Levitate and Burning Hands, to the guy who's the world's greatest diviner and fortune teller as long as he's inebriated. Wizards and Clerics are rare enough that most people won't have ever met a member of those classes personally (though might've walked by one in a crowded city and not known it), but most people know where the nearest Adept or Magician or Magewright lives.
-There are dozens, if not hundreds, of kinds of known magic, and "arcane" magic itself is just an umbrella term for a wide array of practices and traditions. Wizardry and most other arcane-magic users know how to process the magic that is usually considered to be in the wheelhouse of other sorts of casters, but they've compartmentalized them into being spells. So, a wizard casting Telekinesis may well be using Psionics, Power Word Pain is almost certainly Truenaming, Magic Weapon and Fire Shield might (but won't always, see below) tap into Incarnum, Darkness and Shadow Step probably uses Shadow magic, and Protection From Evil can sometimes represent a Wizard who's made a connection with a divine force, and while he or she may not be a true adherent to whatever this entity is, the Wizard has a part of his or her mind or soul that's at peace with how that being sees the world, at least enough that it can grant certain protections. There are many, many other forms of magic than just these, though, many without any given class that's mastered them, though wizards and artificers are often the ones best equipped to tinker with them.
-The Motif Table: I don't have a good name for this and haven't described it much in-game, but as a background element of magic, one popular theory among Wizards and Artificers and some others is that magic (or at least, certain kinds of it) are fueled by motif that are generated from platonic ideals of things. A candle-mage might derive magic from candles and how they are designed, while a mirror-mage might truly understand mirrors to a great degree. Whether there's actually something to this theory, or if it's just a good model to look at things and understand how they work is something that no mage can truly say to have determined (ie., I haven't decided myself yet.)
-Different Methods: Related to how there's a lot of different magics, a lot of them produce similar results. I made a custome pyromancer prestige class, and one of its prerequisites is knowing at least three versions of the same fire spell (so one might have a copy of Burning Hands that balances the frictive forces in the air itself, one that channels energy directly from the elemental plane of fire, and another that works due to a prayer spoken to a god of fire could all work out.) Magic doesn't necessarily work in the same ways, which can sometimes mean that one caster's magic might be snuffed out, while another still has some functional spells that work in different ways.

I could probably talk more, but I think that's more than enough for now.