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**Caster**: Red/Quints - Magic Pen; Yellow/Blue - Cooldown reduction. I don't care if they don't match up. Every caster relies on their abilties and the faster they come up, the better. Getting yourself magic pen reds/quints means that your abilities can hit for full damage at level 1, as you can zero out an enemy's magic resist. When you pick Magic Pen boots (as you should on most AP champs), you'll be significantly ahead. Magic Resist can have your stuff hitting for 25% less. When you zero that out, you can hit like a truck, even at level 1.
**Physical**: Red/Quints - Armor Pen; Yellow/Blue - Attack Speed. The same rules that apply to magic resist, apply to armor as well. You can effectively negate everyone's armor, allowing you to hit like a truck at level one. Also, since most champions rely heavily on their auto attacks, additional attack speed early on helps. You'll notice that both of these sets of runes are designed to be helpful from level 1 all the way into level 18.
**Jungle**: Red/Quints - Armor Pen: Yellow/Blue - Armor. You're going to need armor to survive in the jungle. Keep your same armor pen sets so you can melee minions and put them at 0 armor, doing max damage. The armor lets you properly jungle. Note that there may be a different setup for AP Jungle champs like Amumu or Nunu. You may want to swap your Armor Pen for Magic Pen for the long-term, but you'll still want the armors in the yellow/blue slots to survive those minions.