What Runes for AP and AD?

For your AP Page. Flat AP Quints, Flat Armour Seals, Flat Magic Pen/AD Marks and Flat MR Glyphs. AD Page Flat AD Marks, Flat AD Quints, Flat Armour Seals and Flat MR Glyphs This pretty much covers every champion with just two rune pages.

For AP, I run:

9x Seal of Scaling Health 6x or 9x Glyph of Scaling Cooldown (10% or 15% at Level 18, respectively) 3x Quintessences of Ability Power 9x Mark of Magic Penetration

I like to max out at the 40-45% CDR cap, and generally prefer scaling health because I think it's better for survivability.

For AD, it depends if it's for a bruiser or an ADC, but for ADC, I run:

2x Quintessence of Attack Speed 1x Quintessence of Physical Damage

9x Mark of Physical Damage 9x Seal of Armor 9x Glyph of Attack Speed (or 9x Glyph of Magic Resist)