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Almost every rune you can purchase will give you some benefit, but there are a few rules to follow when picking which ones to buy. Within reason, the scaling runes (runes that give increased benefit as you level) are more powerful than static runes. This rule can be ignored if the rune is important to the early game. For example, static HP runes and HP/MP regen runes are going to give you a large boost early game, much more than the scaling ones would give late game. If you are unsure of what to choose, here are some of the best choices for the varying types of play:
For any character, especially those with powerful ults with long cooldowns (Like Kayle), scaling cooldown reduction runes are a good choice. For a tank, static HP runes will give you a powerful edge early game (Magic resistance runes can be a good idea, especially on magic weak tanks like Rammus). For physical DPS, Armor Penetration is a good choice, and likewise, Magic Penetration is excellent for magical nukers.