I'm tempted to have my answer be Pendragon 5th edition, which basically boils magic down to: "Only NPCs can wield magic, and it does whatever the GM wants it to do." Simple and effective!
But as far as magic systems that are actually, well, systems, I've always had a fondness for GURPS, both in terms of its "default" system, and the many options and permutations available to otherwise choose from.
I've seen the default GURPS system catch flak even from folks who are otherwise fans of the game, but there's something about it that's always appealed to me. It's sort of a relic of the "D&D, only better!" systems you used to see a lot. It's very D&D, with a veritable encyclopedia of spells to choose from, all arranged in escalating hierarchies of power and grouped by spell college. Indeed, the average GURPS mage ends up with a veritable laundry list of spells in his grimoire thanks to the way the prerequisite system works.
But there are some nice little touches of flavor that set the basic GURPS system apart. Spells are cast using Fatigue Points, and if you overspend your FP, the excess comes out of Hit Points. Any system that encourages wizards to push their magic until they start bleeding out of every orifice, veins throbbing in their temples, eyes bulging - well, that's a great system, right there. Plus, if you critically fumble your casting roll, there's a chance you might accidentally summon a demon! So the basic GURPS magic system, despite sharing similar "mundane" qualities with D&D's, has a certain swords-and-sorcery edge to it that I quite like.
But if that's not to the taste of the GM or the needs of the campaign, there is a massive selection of alternate systems to choose from. GURPS Thaumatology collected a bunch of them, and in that book alone you've got systems for ritual magic, rune magic, herbalism, alchemy, ceremonial magic, spirit-guided magic, freeform magic, Hermetic magic. . . And all of it is built within the rules' existing framework, which is one of the great joys of the 4th edition of GURPS. It's just different permutations within the existing system.
My one caveat to all this is that I've never played games such as Mage or Ars Magica, systems that are famous for their flexible, innovative magic systems. It's entirely possible that my vote might change when/if I ever get to play those systems. But for now, I'm going with GURPS.