Most Cost Efficient Runes on Mordekaiser

First off: Health regen runes. They scale extremely well on him. Do not get AP quints, his Q has a 0.4 AP ratio and his E a 0.6 ratio. His ratio's are shit, especially when compared to true mages. Health regen runes are amazing on him and help with his early game laning. Try it out, you will not regret it. The huge buff to your W, which gives you 60 movement speed when you move towards an ally effected by your shield, also makes it to where you are not absolutely required to get movement speed quints either. You are a large, easier to poke than most, target. The ability to regenerate from poke in addition to regening the cost of your spells early is key to victory. Health regen runes do that for you.

Make sure you get 3 points in movement speed masteries, 3 health regen quints. Health regen runes have great gold value on Mordekaiser. Because every health regen item in the game scales either off your health or base health regen, any flat health regen you can get is amazing on him.

Also, due to the way his shield works, armor/mr is amazing on him. His passive is effectively a 2nd health bar. Because of this, mitigation is strong on him compared to raw health.

His reds, as always, magic penetration reds. Magic penetration syncs better with his kit than raw AP, due to his low AP ratios but low CDs and how his ult works.

So, stats to look for in runes:

Core: Health Regen quints, some yellows. And Magic Penetration reds. Situational: VS AD mid, armor and health per 5 seals with scaling magic resist blues. VS Heavy AD Team, armor and health per 5 seals with scaling ap blues. VS AP mid, health per 5 seals with flat mr blues.

General Purpose Mordekaiser Runes: Health Regen quints, Magic pen reds, 5x armor seals, 4x Health Regen seals, 9x flat or scaling mr blues