Which runes are better?
I feel AP is better but if you want to make every single AP stat matter you get magic pen.
Like for a solo AP laner AP runes are the way to go. But for a mage support like bot lane Zyra/Morgana, magic pen would be a better option.
ValyrianBlade1 votesMagic pen marks are better. Ap glyphs are better.
Because they're primary runes - give more stats in gold value overall.
In general though, you want magic pen more vitally. There's limited access to fiat pen and it's not cheap, but it's your main way to burst down a squishy enemy - greatly increasing your damage by a % against these targets.
Hullabaloo9071 votesIf you arnt building a void staff, MP ruins are the way to go Also, if a champ has really high base damages, MP runes are generally better than ap.
RespectPlus1 votesOr really high AP ratios 
EndlessSorcerer1 votesAP Quints.
Magic Pen Marks.
Always.
TheThomTanksWell1 votesI know this thread is old but, the question is still one I hear all the time and honestly one that has to be asked all the time by everyone.
As Hullabloo907 says the higher base damage/lower ratio champs tend to favor Magic Pen over Full AP since they get more out of the Pen. Higher Ratios(Veigar and other nuke types) will almost always benefit from the AP more. However, I have found that play style has just as much to do with it. For instance I do not use defensive runes(no MR or Armor) on most of my pages except tanks. I use triple magic pen(Quints, Marks, AND Glyphs) and let me tell you not having extra MR early is definitely offset by 20|7% Magic Pen out of the gate. Meaning the average mid lane page(that I have seen) has 35-40 starting MR. You ignore 20 of that off the bat and then reduce whats left by 7% for a effective MR(using 40) of 18.6 which is rounded up to 19. Much lower than your starting MR. Meaning while you have slightly less ap you do more damage early with the lower APs that people tend to have at the start of the game. So, my suggestion is if you harass more at level 1-3 then Magic Pen, but if you are more passive then AP.
