Best runes for Zed: Attack damage or Armor penetration?

For Zed, you can last hit VERY easily with your passive. You don't need a full AD rune set. You get maximum killing potential at level 6 which is when you start building items, and this is also the time when armor pen runes start becoming effective. Therefore you should use some armor pen runes. Example setups:

9 Armor pen marks, 3 AD quints

9 AD marks, 3 Armor pen quints

I would not recommend running a FULL armor pen setup because you don't want to be too weak in the early game.

I would refer you to this answer as to why you should prefer Armor penetration in runes and masteries.

Attack damage is easier to get with items and usually, items you are going to run in most Zed's build will have attack damage and few or no armor penetration. Unless you run more than 1 or 2 items with armor penetration in your build, favor armor penetration in your runes and masteries.

Related links :

Armor penetration returns, what it does explained

Armor/Magic Penetration to get an enemy into the negative explained

Example of Armor penetration runes vs AD runes

Wish those links help you better understand the difference.

Attack Damage is better in the current meta. Attack Speed Quints are really popular right now among the high level players. Lifesteal quints got nerfed and aren't as useful. So definitely AD out of the two.

I personally like to run: Armor pen quints, Flat AD Marks, Armor and/or Health seals and mr blues :) been working for me