Well This is a Guide to Mordekaiser. Of course you are free to change any of the things i have done for your own use but this is just the build i use.

The runes i use help with health as Mordekaiser is a health using spell caster. The Mark of Fortitude, Seal of Fortitude and the Greater Quintessence of Vitality help even from the start of the game as it gives you increased health so you can keep pumping those spells The Seal of Vigor helps with the health regen so that you don't have to continually find health packs (dominion) use your healing spell or continually recall. The Glyph of Malice increases your Critical chance while The Glyph of Furor and The Greater Quintessence of Furor increases the damage you Critical strike will do so these runes support each other. The Greater Quintessence of Alacrity can help you dish out more pain when your spells are in cooldown.

Pros
Good damage output/spells
Fun to have a ghost to control to help dish out the pain
Ghost can be used as a 'shield'
not squishy

cons
hard to get used to
people try to gank you
can be annoying controlling the ghost sometimes