Obviously, you want both, but I'm going to be specific about rune pages.
On what champion, or in what matchups, is it worth it to go for penetrations over AD or AP and v/v?
Edit: To clarify, It's pretty obvious that AP marks don't cut it, so think about the quints.
For AP, the mpen marks simply give much greater value than the AP marks.
For AD, armor pen, and attack speed, I believe it that attack speed scales your autoattack best always, armor pen beats AD when you're getting above 100ish AD. Armor pen and AD fuel AD caster skills, attack speed does not.
So I'm no expert by any means, but generally the way to think about it is this: flat ad/ap is strong early, penetration is strong late. If your character is someone who is looking to be strong early, than take flat ad/ap. If it is someone looking to farm and become strong late, take penetration.
