Ars Magica method: Mages are the main characters and are overpowered compared to everyone else. Martial characters are trusted sidekicks. Don't worry about balance.
Classless method: Why can't martial characters also dabble in magic and vice versa?
Magic Item method: Magic can only be cast through magic items with each magical item carrying only one spell that it can cast, so they're more like special abilities that anyone can get. See Errant RPG's use of grimoires.
Magic Is Draining method: Magic spells cost magic points to cast (say 1 to 5 out of 10 to 20 total points a character could have). Magic points recover very slowly (say 1 point per day). When you cast a spell, you better mean it.
Magic Is Hard method: It takes a long time to learn how to cast any given spell, so the only people who know more than X are old. X being 2 or 5 or whatever works.
Magic Is Dangerous method: Mages risk flubbing their spell and Bad Things Happen (TM) when they roll poorly. See Warhammer Fantasy RPG, a lot of OSR retroclones (Dungeon Crawl Classics comes to mind), and a slew of other pen & paper RPGs.
Magic Is Evil method: Magic corrupts you when you use it. Only evil people cast it or casting too much risks you becoming an evil NPC or something like that. See Symbaroum.
Magic Is Weak method: Magic does very minor cantrip-like things only.
Magic Is Chaos method: When you cast a spell, you're not quite sure what's going to happen. More dangerous than Magic Is Dangerous, in that with MID, when you do things right, the results are always the same. With this method, there are no standard results, so who the fuck knows whether that flame spell you're casting will light a candle, light a fireplace, light a fireball, or light the whole city?
Magic Is Inhuman method: Is yous an elf or dragon in a human-only PCs game? No? No magics for you!
Magic Is Slow method: All magic is ritual magic - brewing potions, crafting magic items, performing long rituals, etc. No casting a fireball in the heat of battle. If you want to kill someone, it will be quicker and easier just to stab them than it is to spend the three days casting "Slay That Dude" after collecting all the requisite ingredients, not to mention having to learn That Dude's true name.