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I've only played Runescape for about five months total (current active subscription), but judging from other games I've played, Runescape may have the deepest magic system I've encountered so far.
Not only are there the large variety of combat spells (which other games have), but there is an entire crafting aspect to magic with enchantments that tie it into Runescape's huge economy. It's also part of the travel system through teleports. Casting spells requires the management of different runes as raw material (most game just use a simple mana bar system).
(And these are just from the basic spellbook. I haven't played long enough to get to the higher books).
Has anyone encountered a more complex system than Runescapes?