In lots of forums, ArPen runes are considered the best marks (along with Insight) and AS runes are referred as "do not buy runes". I'm not quite sure why.
9 Tier 3 ArPen runes comes to 11.61 ArPen. Surprisingly, the more Armor an enemy has, the less effect these runes have. I did the maths:
Let's say you have 100 Attack Damage.
If your target has 25 armor (20% reduction), you will deliver 80 damage without ArPen runes.
With ArPen reduction of 11.61 you decrease an enemy's armor to 13.39 (11.8% reduction) and you deliver 88.2 damage. So your ArPen runes gave you 10.2% bonus dmg (88.2 / 80)
But if your target has, let's say 75 armor (42.9% reduction), you will deliver 57.1 damage without runes.
With ArPen runes, your target has 63.39 Armor (38.8% reduction) and you will deliver 61.2 damage, which is only 7.1% more than damage without runes (61.2 / 57.1).
150 armor (60% reduction) = 40 damage // with runes 138.39 armor (58.1% reduction) = 41.9 damage // difference = 4.8%
So we can say, ArPen runes will give you +5-10% extra damage depending on how much armor your enemy has. But AS runes will give you 11.88% more attack speed.
ArPen will further benefit from attack speed and damage. But it only stacks with more ArPen. AS will further benefit from damage and ArPen, but will only stack with more AS. And you will also benefit more from hit-to-apply-affect skills. Of course, AS will not help you much for champions with strong physical skills, like Riven or Garen.
It seems to me that ArPen is better for champions who use lots of AS items or have strong physical skills, but it will be a lot weaker for champions who use damage or ArPen items.
Did I miss something? Because if you find yourself battling against some heavy tank, like Rammus, you can end up having all your marks for ArPen giving you only some minor 3% bonus, instead of a nice 12% attack speed bonus.